Publications
Grabski, H., Grabska, S., & Abagyan, R. (2024). Identifying Allosteric Small-Molecule Binding Sites of Inactive NS2B-NS3 Proteases of Pathogenic Flaviviridae. Viruses, 17(1). https://doi.org/10.3390/v17010006
Grabska, S., Grabski, H., Makunts, T., & Abagyan, R. (2024). Co-Occurring Infections in Cancer Patients Treated with Checkpoint Inhibitors Significantly Increase the Risk of Immune-Related Adverse Events. Cancers, 16(16). https://doi.org/10.3390/cancers16162820
Jarończyk, M., Abagyan, R., & Totrov, M. (2024). Software and Databases for Protein-Protein Docking. Methods in Molecular Biology (Clifton, N.J.), 2780, 129–138. https://doi.org/10.1007/978-1-0716-3985-6_8
Raush, E., Abagyan, R., & Totrov, M. (2024). Efficient Generation of Conformer Ensembles Using Internal Coordinates and a Generative Directional Graph Convolution Neural Network. Journal of Chemical Theory and Computation, 20(9), 4054–4063. https://doi.org/10.1021/acs.jctc.4c00280
Munson, B. P., Chen, M., Bogosian, A., Kreisberg, J. F., Licon, K., Abagyan, R., Kuenzi, B. M., & Ideker, T. (2024). De novo generation of multi-target compounds using deep generative chemistry. Nature Communications, 15(1), 3636. https://doi.org/10.1038/s41467-024-47120-y
Makunts, T., Joulfayan, H., & Abagyan, R. (2024). Thyroid Hyperplasia and Neoplasm Adverse Events Associated With Glucagon-Like Peptide-1 Receptor Agonists in the Food and Drug Administration Adverse Event Reporting System: Retrospective Analysis. JMIRx Med, 5, e55976. https://doi.org/10.2196/55976 (Weight loss may come with thyroid cancer )
Makunts, T., Joulfayan, H., & Abagyan, R. (2024). Authors’ Response to Peer Reviews of “Thyroid Hyperplasia and Neoplasm Adverse Events Associated With Glucagon-Like Peptide-1 Receptor Agonists in the Food and Drug Administration Adverse Event Reporting System: Retrospective Analysis”. JMIRx Med, 5, e58273. https://doi.org/10.2196/58273
Makunts, T., Grabska, S., Grabski, H., & Abagyan, R. (2024). Co-occurring infections in cancer patients treated with checkpoint inhibitors significantly increase the risk of immune related adverse events. In medRxiv: The preprint server for health sciences (p. 2024.02.14.24302840). https://doi.org/10.1101/2024.02.14.24302840
Makunts, T., & Abagyan, R. (2024). Hepatic injury and hepatic failure adverse events in 3,4-methylenedioxymethamphetamine users reported to the FDA Adverse Event Reporting System. Frontiers in Psychiatry, 15, 1414622. https://doi.org/10.3389/fpsyt.2024.1414622
Sauvey, C., Meewan, I., Ehrenkaufer, G., Blevitt, J., Jackson, P., & Abagyan, R. (2023). High-throughput phenotypic screen identifies a new family of potent anti-amoebic compounds. PloS One, 18(5), e0280232. https://doi.org/10.1371/journal.pone.0280232
Meewan, I., Shiryaev, S. A., Kattoula, J., Huang, C.-T., Lin, V., Chuang, C.-H., Terskikh, A. V., & Abagyan, R. (2023). Allosteric Inhibitors of Zika Virus NS2B-NS3 Protease Targeting Protease in “Super-Open” Conformation. Viruses, 15(5). https://doi.org/10.3390/v15051106
Makunts, T., Joulfayan, H., & Abagyan, R. (2023). Thyroid hyperplasia and neoplasm adverse events associated with GLP-1 receptor agonists in FDA Adverse Event Reporting System. In medRxiv: The preprint server for health sciences (p. 2023.11.19.23298750). https://doi.org/10.1101/2023.11.19.23298750
Makunts, T., Dahill, D., Jerome, L., de Boer, A., & Abagyan, R. (2023). Concomitant medications associated with ischemic, hypertensive, and arrhythmic events in MDMA users in FDA adverse event reporting system. Frontiers in Psychiatry, 14, 1149766. https://doi.org/10.3389/fpsyt.2023.1149766
Joulfayan, H., Makunts, T., & Abagyan, R. (2023). Anti-TNF-α therapy induced psoriasis in rheumatoid arthritis patients according to FDA postmarketing surveillance data. Scientific Reports, 13(1), 10448. https://doi.org/10.1038/s41598-023-37010-6
DeForest, N., Kavitha, B., Hu, S., Isaac, R., Krohn, L., Wang, M., Du, X., De Arruda Saldanha, C., Gylys, J., Merli, E., Abagyan, R., Najmi, L., Mohan, V., Flannick, J., Peloso, G. M., Gordts, P. L. S. M., Heinz, S., Deaton, A. M., Khera, A. V., … Majithia, A. R. (2023). Human gain-of-function variants in HNF1A confer protection from diabetes but independently increase hepatic secretion of atherogenic lipoproteins. Cell Genomics, 3(7), 100339. https://doi.org/10.1016/j.xgen.2023.100339
Rosenthal, S. B., Wang, H., Shi, D., Liu, C., Abagyan, R., McEvoy, L. K., & Chen, C.-H. (2022). Mapping the gene network landscape of Alzheimer’s disease through integrating genomics and transcriptomics. PLoS Computational Biology, 18(2), e1009903. https://doi.org/10.1371/journal.pcbi.1009903
Raush, E., Abagyan, R., & Totrov, M. (2022). Graph-Convolutional Neural Net Model of the Statistical Torsion Profiles for Small Organic Molecules. Journal of Chemical Information and Modeling, 62(23), 5896–5906. https://doi.org/10.1021/acs.jcim.2c00790
Meewan, I., Kattoula, J., Kattoula, J. Y., Skinner, D., Fajtová, P., Giardini, M. A., Woodworth, B., McKerrow, J. H., Lage de Siqueira-Neto, J., O’Donoghue, A. J., & Abagyan, R. (2022). Discovery of Triple Inhibitors of Both SARS-CoV-2 Proteases and Human Cathepsin L. Pharmaceuticals (Basel, Switzerland), 15(6). https://doi.org/10.3390/ph15060744
Makunts, T., Burkhart, K., Abagyan, R., & Lee, P. (2022). Retrospective analysis of clinical trial safety data for pembrolizumab reveals the effect of co-occurring infections on immune-related adverse events. PloS One, 17(2), e0263402. https://doi.org/10.1371/journal.pone.0263402
Demuro, S., Sauvey, C., Tripathi, S. K., Di Martino, R. M. C., Shi, D., Ortega, J. A., Russo, D., Balboni, B., Giabbai, B., Storici, P., Girotto, S., Abagyan, R., & Cavalli, A. (2022). ARN25068, a versatile starting point towards triple GSK-3β/FYN/DYRK1A inhibitors to tackle tau-related neurological disorders. European Journal of Medicinal Chemistry, 229, 114054. https://doi.org/10.1016/j.ejmech.2021.114054
Bartholow, T. G., Sztain, T., Young, M. A., Lee, D. J., Davis, T. D., Abagyan, R., & Burkart, M. D. (2022). Control of Unsaturation in De Novo Fatty Acid Biosynthesis by FabA. Biochemistry, 61(7), 608–615. https://doi.org/10.1021/acs.biochem.2c00094
Awdishu, L., & Abagyan, R. (2022). Do Proton-Pump Inhibitors Cause CKD and Progression of CKD?: PRO. Kidney360, 3(7), 1134–1136. https://doi.org/10.34067/KID.0007622021
Xiong, Z., Jeon, M., Allaway, R. J., Kang, J., Park, D., Lee, J., Jeon, H., Ko, M., Jiang, H., Zheng, M., Tan, A. C., Guo, X., Dang, K. K., Tropsha, A., Hecht, C., Das, T. K., Carlson, H. A., Abagyan, R., Guinney, J., … Cagan, R. (2021). Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge. PLoS Computational Biology, 17(9), e1009302. https://doi.org/10.1371/journal.pcbi.1009302
Wollmer, M. A., Makunts, T., Krüger, T. H. C., & Abagyan, R. (2021). Postmarketing safety surveillance data reveals protective effects of botulinum toxin injections against incident anxiety. Scientific Reports, 11(1), 24173. https://doi.org/10.1038/s41598-021-03713-x
Sauvey, C., Ehrenkaufer, G., Shi, D., Debnath, A., & Abagyan, R. (2021). Antineoplastic kinase inhibitors: A new class of potent anti-amoebic compounds. PLoS Neglected Tropical Diseases, 15(2), e0008425. https://doi.org/10.1371/journal.pntd.0008425
Nigam, A. K., Ojha, A. A., Li, J. G., Shi, D., Bhatnagar, V., Nigam, K. B., Abagyan, R., & Nigam, S. K. (2021). Molecular Properties of Drugs Handled by Kidney OATs and Liver OATPs Revealed by Chemoinformatics and Machine Learning: Implications for Kidney and Liver Disease. Pharmaceutics, 13(10). https://doi.org/10.3390/pharmaceutics13101720
Nguyen, V. N., Abagyan, R., & Tsunoda, S. M. (2021). Mtor inhibitors associated with higher cardiovascular adverse events-A large population database analysis. Clinical Transplantation, 35(4), e14228. https://doi.org/10.1111/ctr.14228
Natala, S. R., Habas, A., Stocking, E. M., Orry, A., Price, D. L., Gill, M. B., Bonhaus, D. W., Abagyan, R., & Wrasidlo, W. (2021). Structure based design and synthesis of novel Toll-like Receptor 2 (TLR 2) lipid antagonists. Bioorganic & Medicinal Chemistry Letters, 40, 127861. https://doi.org/10.1016/j.bmcl.2021.127861
Makunts, T., Saunders, I. M., Cohen, I. V., Li, M., Moumedjian, T., Issa, M. A., Burkhart, K., Lee, P., Patel, S. P., & Abagyan, R. (2021). Myocarditis occurrence with cancer immunotherapy across indications in clinical trial and post-marketing data. Scientific Reports, 11(1), 17324. https://doi.org/10.1038/s41598-021-96467-5
Makunts, T., Jerome, L., Abagyan, R., & de Boer, A. (2021). Reported Cases of Serotonin Syndrome in MDMA Users in FAERS Database. Frontiers in Psychiatry, 12, 824288. https://doi.org/10.3389/fpsyt.2021.824288
Keshishi, D., Makunts, T., & Abagyan, R. (2021). Common osteoporosis drug associated with increased rates of depression and anxiety. Scientific Reports, 11(1), 23956. https://doi.org/10.1038/s41598-021-03214-x
He, X., Feng, J., Yan, S., Zhang, Y., Zhong, C., Liu, Y., Shi, D., Abagyan, R., Xiang, T., & Zhang, J. (2021). Biomimetic microbioreactor-supramolecular nanovesicles improve enzyme therapy of hepatic cancer. Nanomedicine : Nanotechnology, Biology, and Medicine, 31, 102311. https://doi.org/10.1016/j.nano.2020.102311
Cohen, I. V., Makunts, T., Abagyan, R., & Thomas, K. (2021). Concomitant drugs associated with increased mortality for MDMA users reported in a drug safety surveillance database. Scientific Reports, 11(1), 5997. https://doi.org/10.1038/s41598-021-85389-x
Bartholow, T. G., Sztain, T., Young, M. A., Davis, T. D., Abagyan, R., & Burkart, M. D. (2021). Protein-protein interaction based substrate control in the E. coli octanoic acid transferase, LipB. RSC Chemical Biology, 2(5), 1466–1473. https://doi.org/10.1039/d1cb00125f
Bartholow, T. G., Sztain, T., Patel, A., Lee, D. J., Young, M. A., Abagyan, R., & Burkart, M. D. (2021). Elucidation of transient protein-protein interactions within carrier protein-dependent biosynthesis. Communications Biology, 4(1), 340. https://doi.org/10.1038/s42003-021-01838-3
Yang, L., Zhang, Y., Xie, J., Zhong, C., He, D., Wang, T., Li, K., Li, Y., Shi, D., Abagyan, R., Yang, L., & Zhang, J. (2020). Biomimetic polysaccharide-cloaked lipidic nanovesicles/microassemblies for improving the enzymatic activity and prolonging the action time for hyperuricemia treatment. Nanoscale, 12(28), 15222–15235. https://doi.org/10.1039/d0nr02651d
Steinbrenner, A. D., Muñoz-Amatriaín, M., Chaparro, A. F., Aguilar-Venegas, J. M., Lo, S., Okuda, S., Glauser, G., Dongiovanni, J., Shi, D., Hall, M., Crubaugh, D., Holton, N., Zipfel, C., Abagyan, R., Turlings, T. C. J., Close, T. J., Huffaker, A., & Schmelz, E. A. (2020). A receptor-like protein mediates plant immune responses to herbivore-associated molecular patterns. Proceedings of the National Academy of Sciences of the United States of America, 117(49), 31510–31518. https://doi.org/10.1073/pnas.2018415117
Poretsky, E., Dressano, K., Weckwerth, P., Ruiz, M., Char, S. N., Shi, D., Abagyan, R., Yang, B., & Huffaker, A. (2020). Differential activities of maize plant elicitor peptides as mediators of immune signaling and herbivore resistance. The Plant Journal : For Cell and Molecular Biology, 104(6), 1582–1602. https://doi.org/10.1111/tpj.15022
Nigam, A. K., Li, J. G., Lall, K., Shi, D., Bush, K. T., Bhatnagar, V., Abagyan, R., & Nigam, S. K. (2020). Unique metabolite preferences of the drug transporters OAT1 and OAT3 analyzed by machine learning. The Journal of Biological Chemistry, 295(7), 1829–1842. https://doi.org/10.1074/jbc.RA119.010729
Nicola, G., Kufareva, I., Ilatovskiy, A. V., & Abagyan, R. (2020). Druggable exosites of the human kino-pocketome. Journal of Computer-Aided Molecular Design, 34(3), 219–230. https://doi.org/10.1007/s10822-019-00276-y
Ngo, T., Stephens, B. S., Gustavsson, M., Holden, L. G., Abagyan, R., Handel, T. M., & Kufareva, I. (2020). Crosslinking-guided geometry of a complete CXC receptor-chemokine complex and the basis of chemokine subfamily selectivity. PLoS Biology, 18(4), e3000656. https://doi.org/10.1371/journal.pbio.3000656
Makunts, T., Wollmer, M. A., & Abagyan, R. (2020). Postmarketing safety surveillance data reveals antidepressant effects of botulinum toxin across various indications and injection sites. Scientific Reports, 10(1), 12851. https://doi.org/10.1038/s41598-020-69773-7
Makunts, T., & Abagyan, R. (2020). How can proton pump inhibitors damage central and peripheral nervous systems? Neural Regeneration Research, 15(11), 2041–2042. https://doi.org/10.4103/1673-5374.282252
Lebouvier, N., Pagniez, F., Na, Y. M., Shi, D., Pinson, P., Marchivie, M., Guillon, J., Hakki, T., Bernhardt, R., Yee, S. W., Simons, C., Lézé, M.-P., Hartmann, R. W., Mularoni, A., Le Baut, G., Krimm, I., Abagyan, R., Le Pape, P., & Le Borgne, M. (2020). Synthesis, Optimization, Antifungal Activity, Selectivity, and CYP51 Binding of New 2-Aryl-3-azolyl-1-indolyl-propan-2-ols. Pharmaceuticals (Basel, Switzerland), 13(8). https://doi.org/10.3390/ph13080186
Huang, Y., Gu, J., Yan, Z., Hu, X., He, D., Zhang, Y., Li, Y., Zhong, C., Yang, J., Shi, D., Abagyan, R., Tan, Q., & Zhang, J. (2020). Cytomembrane-mimicking nanocarriers with a scaffold consisting of a CD44-targeted endogenous component for effective asparaginase supramolecule delivery. Nanoscale, 12(22), 12083–12097. https://doi.org/10.1039/d0nr02588g
Hahn, H. J., Abagyan, R., Podust, L. M., Roy, S., Ali, I. K. M., & Debnath, A. (2020). HMG-CoA Reductase Inhibitors as Drug Leads against Naegleria fowleri. ACS Chemical Neuroscience, 11(19), 3089–3096. https://doi.org/10.1021/acschemneuro.0c00428
Gu, J., Huang, Y., Yan, Z., He, D., Zhang, Y., Xu, J., Li, Y., Xie, X., Xie, J., Shi, D., Abagyan, R., Zhang, J., & Tan, Q. (2020). Biomimetic Membrane-Structured Nanovesicles Carrying a Supramolecular Enzyme to Cure Lung Cancer. ACS Applied Materials & Interfaces, 12(28), 31112–31123. https://doi.org/10.1021/acsami.0c06207
Graña, E., Díaz-Tielas, C., Sánchez-Moreiras, A. M., Reigosa, M. J., Celeiro, M., Abagyan, R., Teijeira, M., Duke, M. V., Clerk, T., Pan, Z., & Duke, S. O. (2020). Transcriptome and binding data indicate that citral inhibits single strand DNA-binding proteins. Physiologia Plantarum, 169(1), 99–109. https://doi.org/10.1111/ppl.13055
Escher, B. I., Abagyan, R., Embry, M., Klüver, N., Redman, A. D., Zarfl, C., & Parkerton, T. F. (2020). Recommendations for Improving Methods and Models for Aquatic Hazard Assessment of Ionizable Organic Chemicals. Environmental Toxicology and Chemistry, 39(2), 269–286. https://doi.org/10.1002/etc.4602
Engelhart, D. C., Granados, J. C., Shi, D., Saier Jr, M. H. J., Baker, M. E., Abagyan, R., & Nigam, S. K. (2020). Systems Biology Analysis Reveals Eight SLC22 Transporter Subgroups, Including OATs, OCTs, and OCTNs. International Journal of Molecular Sciences, 21(5). https://doi.org/10.3390/ijms21051791
Cohen, I. V., Makunts, T., Moumedjian, T., Issa, M. A., & Abagyan, R. (2020). Cardiac adverse events associated with chloroquine and hydroxychloroquine exposure in 20 years of drug safety surveillance reports. Scientific Reports, 10(1), 19199. https://doi.org/10.1038/s41598-020-76258-0
Zhang, Y., Shi, D., Abagyan, R., Dai, W., & Dong, M. (2019). Population Scale Retrospective Analysis Reveals Potential Risk of Cholestasis in Pregnant Women Taking Omeprazole, Lansoprazole, and Amoxicillin. Interdisciplinary Sciences, Computational Life Sciences, 11(2), 273–281. https://doi.org/10.1007/s12539-019-00335-w
Shi, D., Khan, F., & Abagyan, R. (2019). Extended Multitarget Pharmacology of Anticancer Drugs. Journal of Chemical Information and Modeling, 59(6), 3006–3017. https://doi.org/10.1021/acs.jcim.9b00031
Shi, D., Chahal, K. K., Oto, P., Nothias, L.-F., Debnath, A., McKerrow, J. H., Podust, L. M., & Abagyan, R. (2019). Identification of Four Amoebicidal Nontoxic Compounds by a Molecular Docking Screen of Naegleria fowleri Sterol Δ8-Δ7-Isomerase and Phenotypic Assays. ACS Infectious Diseases, 5(12), 2029–2038. https://doi.org/10.1021/acsinfecdis.9b00227
Naz, S., Farooq, U., Ali, S., Sarwar, R., Khan, S., & Abagyan, R. (2019). Identification of new benzamide inhibitor against α-subunit of tryptophan synthase from Mycobacterium tuberculosis through structure-based virtual screening, anti-tuberculosis activity and molecular dynamics simulations. Journal of Biomolecular Structure & Dynamics, 37(4), 1043–1053. https://doi.org/10.1080/07391102.2018.1448303
Meewan, I., Zhang, X., Roy, S., Ballatore, C., O’Donoghue, A. J., Schooley, R. T., & Abagyan, R. (2019). Discovery of New Inhibitors of Hepatitis C Virus NS3/4A Protease and Its D168A Mutant. ACS Omega, 4(16), 16999–17008. https://doi.org/10.1021/acsomega.9b02491
Makunts, T., U, A., Atayee, R. S., & Abagyan, R. (2019). Retrospective analysis reveals significant association of hypoglycemia with tramadol and methadone in contrast to other opioids. Scientific Reports, 9(1), 12490. https://doi.org/10.1038/s41598-019-48955-y
Makunts, T., Cohen, I. V., Awdishu, L., & Abagyan, R. (2019). Analysis of postmarketing safety data for proton-pump inhibitors reveals increased propensity for renal injury, electrolyte abnormalities, and nephrolithiasis. Scientific Reports, 9(1), 2282. https://doi.org/10.1038/s41598-019-39335-7
Makunts, T., Alpatty, S., Lee, K. C., Atayee, R. S., & Abagyan, R. (2019). Proton-pump inhibitor use is associated with a broad spectrum of neurological adverse events including impaired hearing, vision, and memory. Scientific Reports, 9(1), 17280. https://doi.org/10.1038/s41598-019-53622-3
Maccesi, M., Aguiar, P. H. N., Pasche, V., Padilla, M., Suzuki, B. M., Montefusco, S., Abagyan, R., Keiser, J., Mourão, M. M., & Caffrey, C. R. (2019). Multi-center screening of the Pathogen Box collection for schistosomiasis drug discovery. Parasites & Vectors, 12(1), 493. https://doi.org/10.1186/s13071-019-3747-6
Lam, P. C.-H., Abagyan, R., & Totrov, M. (2019). Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4. Journal of Computer-Aided Molecular Design, 33(12), 1057–1069. https://doi.org/10.1007/s10822-019-00225-9
Lam, P. C.-H., Abagyan, R., & Totrov, M. (2019). Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3. Journal of Computer-Aided Molecular Design, 33(1), 35–46. https://doi.org/10.1007/s10822-018-0139-5
Kufareva, I., Bestgen, B., Brear, P., Prudent, R., Laudet, B., Moucadel, V., Ettaoussi, M., Sautel, C. F., Krimm, I., Engel, M., Filhol, O., Borgne, M. L., Lomberget, T., Cochet, C., & Abagyan, R. (2019). Discovery of holoenzyme-disrupting chemicals as substrate-selective CK2 inhibitors. Scientific Reports, 9(1), 15893. https://doi.org/10.1038/s41598-019-52141-5
Desai, A. J., Mechin, I., Nagarajan, K., Valant, C., Wootten, D., Lam, P. C. H., Orry, A., Abagyan, R., Nair, A., Sexton, P. M., Christopoulos, A., & Miller, L. J. (2019). Molecular Basis of Action of a Small-Molecule Positive Allosteric Modulator Agonist at the Type 1 Cholecystokinin Holoreceptor. Molecular Pharmacology, 95(3), 245–259. https://doi.org/10.1124/mol.118.114082
Chahal, K. K., Li, J., Kufareva, I., Parle, M., Durden, D. L., Wechsler-Reya, R. J., Chen, C. C., & Abagyan, R. (2019). Nilotinib, an approved leukemia drug, inhibits smoothened signaling in Hedgehog-dependent medulloblastoma. PloS One, 14(9), e0214901. https://doi.org/10.1371/journal.pone.0214901
Bestgen, B., Kufareva, I., Seetoh, W., Abell, C., Hartmann, R. W., Abagyan, R., Le Borgne, M., Filhol, O., Cochet, C., Lomberget, T., & Engel, M. (2019). 2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 2. Structure-Based Optimization and Investigation of Effects Specific to the Allosteric Mode of Action. Journal of Medicinal Chemistry, 62(4), 1817–1836. https://doi.org/10.1021/acs.jmedchem.8b01765
Bestgen, B., Krimm, I., Kufareva, I., Kamal, A. A. M., Seetoh, W.-G., Abell, C., Hartmann, R. W., Abagyan, R., Cochet, C., Le Borgne, M., Engel, M., & Lomberget, T. (2019). 2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 1. Identification of an Allosteric Binding Site. Journal of Medicinal Chemistry, 62(4), 1803–1816. https://doi.org/10.1021/acs.jmedchem.8b01766
Svetlov, D., Shi, D., Twentyman, J., Nedialkov, Y., Rosen, D. A., Abagyan, R., & Artsimovitch, I. (2018). In silico discovery of small molecules that inhibit RfaH recruitment to RNA polymerase. Molecular Microbiology, 110(1), 128–142. https://doi.org/10.1111/mmi.14093
Makunts, T., Cohen, I. V., Lee, K. C., & Abagyan, R. (2018). Population scale retrospective analysis reveals distinctive antidepressant and anxiolytic effects of diclofenac, ketoprofen and naproxen in patients with pain. PloS One, 13(4), e0195521. https://doi.org/10.1371/journal.pone.0195521
Lam, P. C.-H., Abagyan, R., & Totrov, M. (2018). Ligand-biased ensemble receptor docking (LigBEnD): A hybrid ligand/receptor structure-based approach. Journal of Computer-Aided Molecular Design, 32(1), 187–198. https://doi.org/10.1007/s10822-017-0058-x
Kauppi, K., Rosenthal, S. B., Lo, M.-T., Sanyal, N., Jiang, M., Abagyan, R., McEvoy, L. K., Andreassen, O. A., & Chen, C.-H. (2018). Revisiting Antipsychotic Drug Actions Through Gene Networks Associated With Schizophrenia. The American Journal of Psychiatry, 175(7), 674–682. https://doi.org/10.1176/appi.ajp.2017.17040410
Chahal, K. K., Parle, M., & Abagyan, R. (2018). Dexamethasone and Fludrocortisone Inhibit Hedgehog Signaling in Embryonic Cells. ACS Omega, 3(9), 12019–12025. https://doi.org/10.1021/acsomega.8b01864
Chahal, K. K., Parle, M., & Abagyan, R. (2018). Hedgehog pathway and smoothened inhibitors in cancer therapies. Anti-Cancer Drugs, 29(5), 387–401. https://doi.org/10.1097/CAD.0000000000000609
Arnautova, Y. A., Abagyan, R., & Totrov, M. (2018). Protein-RNA Docking Using ICM. Journal of Chemical Theory and Computation, 14(9), 4971–4984. https://doi.org/10.1021/acs.jctc.8b00293
Zheng, Y., Han, G. W., Abagyan, R., Wu, B., Stevens, R. C., Cherezov, V., Kufareva, I., & Handel, T. M. (2017). Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV. Immunity, 46(6), 1005-1017.e5. https://doi.org/10.1016/j.immuni.2017.05.002
Warszycki, D., Rueda, M., Mordalski, S., Kristiansen, K., Satała, G., Rataj, K., Chilmonczyk, Z., Sylte, I., Abagyan, R., & Bojarski, A. J. (2017). From Homology Models to a Set of Predictive Binding Pockets-a 5-HT(1A) Receptor Case Study. Journal of Chemical Information and Modeling, 57(2), 311–321. https://doi.org/10.1021/acs.jcim.6b00263
Sun, N., Lu, Y.-J., Chan, F.-Y., Du, R.-L., Zheng, Y.-Y., Zhang, K., So, L.-Y., Abagyan, R., Zhuo, C., Leung, Y.-C., & Wong, K.-Y. (2017). A Thiazole Orange Derivative Targeting the Bacterial Protein FtsZ Shows Potent Antibacterial Activity. Frontiers in Microbiology, 8, 855. https://doi.org/10.3389/fmicb.2017.00855
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Parsonage, D., Sheng, F., Hirata, K., Debnath, A., McKerrow, J. H., Reed, S. L., Abagyan, R., Poole, L. B., & Podust, L. M. (2016). X-ray structures of thioredoxin and thioredoxin reductase from Entamoeba histolytica and prevailing hypothesis of the mechanism of Auranofin action. Journal of Structural Biology, 194(2), 180–190. https://doi.org/10.1016/j.jsb.2016.02.015
Pallara, C., Rueda, M., Abagyan, R., & Fernández-Recio, J. (2016). Conformational Heterogeneity of Unbound Proteins Enhances Recognition in Protein-Protein Encounters. Journal of Chemical Theory and Computation, 12(7), 3236–3249. https://doi.org/10.1021/acs.jctc.6b00204
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Liu, H. C., Jamshidi, N., Chen, Y., Eraly, S. A., Cho, S. Y., Bhatnagar, V., Wu, W., Bush, K. T., Abagyan, R., Palsson, B. O., & Nigam, S. K. (2016). An Organic Anion Transporter 1 (OAT1)-centered Metabolic Network. The Journal of Biological Chemistry, 291(37), 19474–19486. https://doi.org/10.1074/jbc.M116.745216
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Leach, K., Gregory, K. J., Kufareva, I., Khajehali, E., Cook, A. E., Abagyan, R., Conigrave, A. D., Sexton, P. M., & Christopoulos, A. (2016). Towards a structural understanding of allosteric drugs at the human calcium-sensing receptor. Cell Research, 26(5), 574–592. https://doi.org/10.1038/cr.2016.36
Dong, M., Lam, P. C.-H., Orry, A., Sexton, P. M., Christopoulos, A., Abagyan, R., & Miller, L. J. (2016). Use of Cysteine Trapping to Map Spatial Approximations between Residues Contributing to the Helix N-capping Motif of Secretin and Distinct Residues within Each of the Extracellular Loops of Its Receptor. The Journal of Biological Chemistry, 291(10), 5172–5184. https://doi.org/10.1074/jbc.M115.706010
Bennett, B. C., Purdy, M. D., Baker, K. A., Acharya, C., McIntire, W. E., Stevens, R. C., Zhang, Q., Harris, A. L., Abagyan, R., & Yeager, M. (2016). An electrostatic mechanism for Ca(2+)-mediated regulation of gap junction channels. Nature Communications, 7, 8770. https://doi.org/10.1038/ncomms9770
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Qin, L., Kufareva, I., Holden, L. G., Wang, C., Zheng, Y., Zhao, C., Fenalti, G., Wu, H., Han, G. W., Cherezov, V., Abagyan, R., Stevens, R. C., & Handel, T. M. (2015). Structural biology. Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine. Science (New York, N.Y.), 347(6226), 1117–1122. https://doi.org/10.1126/science.1261064
Mayevu, N. M. I., Choe, H., Abagyan, R., Seong, J. Y., Millar, R. P., Katz, A. A., & Flanagan, C. A. (2015). Histidine(7.36(305)) in the conserved peptide receptor activation domain of the gonadotropin releasing hormone receptor couples peptide binding and receptor activation. Molecular and Cellular Endocrinology, 402, 95–106. https://doi.org/10.1016/j.mce.2015.01.008
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Lenoir, M., Kufareva, I., Abagyan, R., & Overduin, M. (2015). Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily. Membranes, 5(4), 646–663. https://doi.org/10.3390/membranes5040646
Kufareva, I., Handel, T. M., & Abagyan, R. (2015). Experiment-Guided Molecular Modeling of Protein-Protein Complexes Involving GPCRs. Methods in Molecular Biology (Clifton, N.J.), 1335, 295–311. https://doi.org/10.1007/978-1-4939-2914-6_19
Husby, J., Bottegoni, G., Kufareva, I., Abagyan, R., & Cavalli, A. (2015). Structure-based predictions of activity cliffs. Journal of Chemical Information and Modeling, 55(5), 1062–1076. https://doi.org/10.1021/ci500742b
Giacoppo, J. O. S., C C França, T., Kuča, K., da Cunha, E. F. F., Abagyan, R., Mancini, D. T., & Ramalho, T. C. (2015). Molecular modeling and in vitro reactivation study between the oxime BI-6 and acetylcholinesterase inhibited by different nerve agents. Journal of Biomolecular Structure & Dynamics, 33(9), 2048–2058. https://doi.org/10.1080/07391102.2014.989408
Geidl, S., Svobodová Vařeková, R., Bendová, V., Petrusek, L., Ionescu, C.-M., Jurka, Z., Abagyan, R., & Koča, J. (2015). How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction? Journal of Chemical Information and Modeling, 55(6), 1088–1097. https://doi.org/10.1021/ci500758w
Geidl, S., Bouchal, T., Raček, T., Svobodová Vařeková, R., Hejret, V., Křenek, A., Abagyan, R., & Koča, J. (2015). High-quality and universal empirical atomic charges for chemoinformatics applications. Journal of Cheminformatics, 7, 59. https://doi.org/10.1186/s13321-015-0107-1
Dong, M., Vattelana, A. M., Lam, P. C.-H., Orry, A. J., Abagyan, R., Christopoulos, A., Sexton, P. M., Haines, D. R., & Miller, L. J. (2015). Development of a highly selective allosteric antagonist radioligand for the type 1 cholecystokinin receptor and elucidation of its molecular basis of binding. Molecular Pharmacology, 87(1), 130–140. https://doi.org/10.1124/mol.114.095430
Desai, A. J., Lam, P. C. H., Orry, A., Abagyan, R., Christopoulos, A., Sexton, P. M., & Miller, L. J. (2015). Molecular Mechanism of Action of Triazolobenzodiazepinone Agonists of the Type 1 Cholecystokinin Receptor. Possible Cooperativity across the Receptor Homodimeric Complex. Journal of Medicinal Chemistry, 58(24), 9562–9577. https://doi.org/10.1021/acs.jmedchem.5b01110
Arnautova, Y. A., Abagyan, R., & Totrov, M. (2015). All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins. Journal of Chemical Theory and Computation, 11(5), 2167–2186. https://doi.org/10.1021/ct501138c
Ali, T. B., Schleret, T. R., Reilly, B. M., Chen, W. Y., & Abagyan, R. (2015). Adverse Effects of Cholinesterase Inhibitors in Dementia, According to the Pharmacovigilance Databases of the United-States and Canada. PloS One, 10(12), e0144337. https://doi.org/10.1371/journal.pone.0144337
Wang, Y., Chan, F.-Y., Sun, N., Lui, H.-K., So, P.-K., Yan, S.-C., Chan, K.-F., Chiou, J., Chen, S., Abagyan, R., Leung, Y.-C., & Wong, K.-Y. (2014). Structure-based design, synthesis, and biological evaluation of isatin derivatives as potential glycosyltransferase inhibitors. Chemical Biology & Drug Design, 84(6), 685–696. https://doi.org/10.1111/cbdd.12361
Sun, N., Chan, F.-Y., Lu, Y.-J., Neves, M. A. C., Lui, H.-K., Wang, Y., Chow, K.-Y., Chan, K.-F., Yan, S.-C., Leung, Y.-C., Abagyan, R., Chan, T.-H., & Wong, K.-Y. (2014). Rational design of berberine-based FtsZ inhibitors with broad-spectrum antibacterial activity. PloS One, 9(5), e97514. https://doi.org/10.1371/journal.pone.0097514
Shmelkov, E., Grigoryan, A., Krachmarov, C., Abagyan, R., & Cardozo, T. (2014). Sequence-conserved and antibody-accessible sites in the V1V2 domain of HIV-1 gp120 envelope protein. AIDS Research and Human Retroviruses, 30(9), 927–931. https://doi.org/10.1089/AID.2014.0034
McRobb, F. M., Sahagún, V., Kufareva, I., & Abagyan, R. (2014). In silico analysis of the conservation of human toxicity and endocrine disruption targets in aquatic species. Environmental Science & Technology, 48(3), 1964–1972. https://doi.org/10.1021/es404568a
McRobb, F. M., Kufareva, I., & Abagyan, R. (2014). In silico identification and pharmacological evaluation of novel endocrine disrupting chemicals that act via the ligand-binding domain of the estrogen receptor α. Toxicological Sciences : An Official Journal of the Society of Toxicology, 141(1), 188–197. https://doi.org/10.1093/toxsci/kfu114
Matos, K. S., da Cunha, E. F. F., Abagyan, R., & Ramalho, T. C. (2014). Computational evidence for the reactivation process of human acetylcholinesterase inhibited by carbamates. Combinatorial Chemistry & High Throughput Screening, 17(6), 554–564. https://doi.org/10.2174/1386207316666131217100416
Lin, C., Ear, J., Midde, K., Lopez-Sanchez, I., Aznar, N., Garcia-Marcos, M., Kufareva, I., Abagyan, R., & Ghosh, P. (2014). Structural basis for activation of trimeric Gi proteins by multiple growth factor receptors via GIV/Girdin. Molecular Biology of the Cell, 25(22), 3654–3671. https://doi.org/10.1091/mbc.E14-05-0978
Kufareva, I., Stephens, B. S., Holden, L. G., Qin, L., Zhao, C., Kawamura, T., Abagyan, R., & Handel, T. M. (2014). Stoichiometry and geometry of the CXC chemokine receptor 4 complex with CXC ligand 12: Molecular modeling and experimental validation. Proceedings of the National Academy of Sciences of the United States of America, 111(50), E5363-5372. https://doi.org/10.1073/pnas.1417037111
Kufareva, I., Lenoir, M., Dancea, F., Sridhar, P., Raush, E., Bissig, C., Gruenberg, J., Abagyan, R., & Overduin, M. (2014). Discovery of novel membrane binding structures and functions. Biochemistry and Cell Biology = Biochimie et Biologie Cellulaire, 92(6), 555–563. https://doi.org/10.1139/bcb-2014-0074
Kufareva, I., Katritch, V., Stevens, R. C., & Abagyan, R. (2014). Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: Meeting new challenges. Structure (London, England : 1993), 22(8), 1120–1139. https://doi.org/10.1016/j.str.2014.06.012
Kennedy, D. P., McRobb, F. M., Leonhardt, S. A., Purdy, M., Figler, H., Marshall, M. A., Chordia, M., Figler, R., Linden, J., Abagyan, R., & Yeager, M. (2014). The second extracellular loop of the adenosine A1 receptor mediates activity of allosteric enhancers. Molecular Pharmacology, 85(2), 301–309. https://doi.org/10.1124/mol.113.088682
Kawamura, T., Stephens, B., Qin, L., Yin, X., Dores, M. R., Smith, T. H., Grimsey, N., Abagyan, R., Trejo, J., Kufareva, I., Fuster, M. M., Salanga, C. L., & Handel, T. M. (2014). A general method for site specific fluorescent labeling of recombinant chemokines. PloS One, 9(1), e81454. https://doi.org/10.1371/journal.pone.0081454
Gabrielsen, M., Kurczab, R., Siwek, A., Wolak, M., Ravna, A. W., Kristiansen, K., Kufareva, I., Abagyan, R., Nowak, G., Chilmonczyk, Z., Sylte, I., & Bojarski, A. J. (2014). Identification of novel serotonin transporter compounds by virtual screening. Journal of Chemical Information and Modeling, 54(3), 933–943. https://doi.org/10.1021/ci400742s
Chernyshev, V. M., Chernysheva, A. V., Abagyan, R. S., & Rybakov, V. B. (2014). Crystal structure of bis-[(5-amino-1H-1,2,4-triazol-3-yl-κN (4))acetato-κO]di-aqua-nickel(II) dihydrate. Acta Crystallographica. Section E, Structure Reports Online, 70(Pt 11), 286–289. https://doi.org/10.1107/S1600536814021436
Chen, Y.-C., Totrov, M., & Abagyan, R. (2014). Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping. Future Medicinal Chemistry, 6(16), 1741–1755. https://doi.org/10.4155/fmc.14.113
Acharya, C., Kufareva, I., Ilatovskiy, A. V., & Abagyan, R. (2014). PeptiSite: A structural database of peptide binding sites in 4D. Biochemical and Biophysical Research Communications, 445(4), 717–723. https://doi.org/10.1016/j.bbrc.2013.12.132
Vařeková, R. S., Geidl, S., Ionescu, C.-M., Skřehota, O., Bouchal, T., Sehnal, D., Abagyan, R., & Koča, J. (2013). Predicting p Ka values from EEM atomic charges. Journal of Cheminformatics, 5(1), 18. https://doi.org/10.1186/1758-2946-5-18
Stevens, R. C., Cherezov, V., Katritch, V., Abagyan, R., Kuhn, P., Rosen, H., & Wüthrich, K. (2013). The GPCR Network: A large-scale collaboration to determine human GPCR structure and function. Nature Reviews. Drug Discovery, 12(1), 25–34. https://doi.org/10.1038/nrd3859
Schug, T. T., Abagyan, R., Blumberg, B., Collins, T. J., Crews, D., DeFur, P. L., Dickerson, S. M., Edwards, T. M., Gore, A. C., Guillette, L. J., Hayes, T., Heindel, J. J., Moores, A., Patisaul, H. B., Tal, T. L., Thayer, K. A., Vandenberg, L. N., Warner, J., Watson, C. S., … Myers, J. P. (2013). Designing Endocrine Disruption Out of the Next Generation of Chemicals. Green Chemistry : An International Journal and Green Chemistry Resource : GC, 15(1), 181–198. https://doi.org/10.1039/C2GC35055F
Rueda, M., Orozco, M., Totrov, M., & Abagyan, R. (2013). BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry. BMC Structural Biology, 13, 32. https://doi.org/10.1186/1472-6807-13-32
Montaner, S., Kufareva, I., Abagyan, R., & Gutkind, J. S. (2013). Molecular mechanisms deployed by virally encoded G protein-coupled receptors in human diseases. Annual Review of Pharmacology and Toxicology, 53, 331–354. https://doi.org/10.1146/annurev-pharmtox-010510-100608
Lindin, I., Wuxiuer, Y., Kufareva, I., Abagyan, R., Moens, U., Sylte, I., & Ravna, A. W. (2013). Homology modeling and ligand docking of Mitogen-activated protein kinase-activated protein kinase 5 (MK5). Theoretical Biology & Medical Modelling, 10, 56. https://doi.org/10.1186/1742-4682-10-56
Lane, J. R., Chubukov, P., Liu, W., Canals, M., Cherezov, V., Abagyan, R., Stevens, R. C., & Katritch, V. (2013). Structure-based ligand discovery targeting orthosteric and allosteric pockets of dopamine receptors. Molecular Pharmacology, 84(6), 794–807. https://doi.org/10.1124/mol.113.088054
Kufareva, I., Stephens, B., Gilliland, C. T., Wu, B., Fenalti, G., Hamel, D., Stevens, R. C., Abagyan, R., & Handel, T. M. (2013). A novel approach to quantify G-protein-coupled receptor dimerization equilibrium using bioluminescence resonance energy transfer. Methods in Molecular Biology (Clifton, N.J.), 1013, 93–127. https://doi.org/10.1007/978-1-62703-426-5_7
Katiyar, S., Kufareva, I., Behera, R., Thomas, S. M., Ogata, Y., Pollastri, M., Abagyan, R., & Mensa-Wilmot, K. (2013). Lapatinib-binding protein kinases in the African trypanosome: Identification of cellular targets for kinase-directed chemical scaffolds. PloS One, 8(2), e56150. https://doi.org/10.1371/journal.pone.0056150
Ilatovskiy, A. V., Abagyan, R., & Kufareva, I. (2013). Quantum Mechanics Approaches to Drug Research in the Era of Structural Chemogenomics. International Journal of Quantum Chemistry, 113(12), 1669–1675. https://doi.org/10.1002/qua.24400
Harikumar, K. G., Cawston, E. E., Lam, P. C. H., Patil, A., Orry, A., Henke, B. R., Abagyan, R., Christopoulos, A., Sexton, P. M., & Miller, L. J. (2013). Molecular basis for benzodiazepine agonist action at the type 1 cholecystokinin receptor. The Journal of Biological Chemistry, 288(29), 21082–21095. https://doi.org/10.1074/jbc.M113.480715
Gabrielsen, M., Wołosewicz, K., Zawadzka, A., Kossakowski, J., Nowak, G., Wolak, M., Stachowicz, K., Siwek, A., Ravna, A. W., Kufareva, I., Kozerski, L., Bednarek, E., Sitkowski, J., Bocian, W., Abagyan, R., Bojarski, A. J., Sylte, I., & Chilmonczyk, Z. (2013). Synthesis, antidepressant evaluation and docking studies of long-chain alkylnitroquipazines as serotonin transporter inhibitors. Chemical Biology & Drug Design, 81(6), 695–706. https://doi.org/10.1111/cbdd.12116
Chan, F.-Y., Sun, N., Neves, M. A. C., Lam, P. C.-H., Chung, W.-H., Wong, L.-K., Chow, H.-Y., Ma, D.-L., Chan, P.-H., Leung, Y.-C., Chan, T.-H., Abagyan, R., & Wong, K.-Y. (2013). Identification of a new class of FtsZ inhibitors by structure-based design and in vitro screening. Journal of Chemical Information and Modeling, 53(8), 2131–2140. https://doi.org/10.1021/ci400203f
Bissig, C., Lenoir, M., Velluz, M.-C., Kufareva, I., Abagyan, R., Overduin, M., & Gruenberg, J. (2013). Viral infection controlled by a calcium-dependent lipid-binding module in ALIX. Developmental Cell, 25(4), 364–373. https://doi.org/10.1016/j.devcel.2013.04.003
Wein, A. N., Williams, B. N., Liu, S., Ermolinsky, B., Provenzano, D., Abagyan, R., Orry, A., Leppla, S. H., & Peredelchuk, M. (2012). Small molecule inhibitors of Bacillus anthracis protective antigen proteolytic activation and oligomerization. Journal of Medicinal Chemistry, 55(18), 7998–8006. https://doi.org/10.1021/jm300804e
Tosh, D. K., Phan, K., Gao, Z.-G., Gakh, A. A., Xu, F., Deflorian, F., Abagyan, R., Stevens, R. C., Jacobson, K. A., & Katritch, V. (2012). Optimization of adenosine 5’-carboxamide derivatives as adenosine receptor agonists using structure-based ligand design and fragment screening. Journal of Medicinal Chemistry, 55(9), 4297–4308. https://doi.org/10.1021/jm300095s
Sager, G., Ørvoll, E. Ø., Lysaa, R. A., Kufareva, I., Abagyan, R., & Ravna, A. W. (2012). Novel cGMP efflux inhibitors identified by virtual ligand screening (VLS) and confirmed by experimental studies. Journal of Medicinal Chemistry, 55(7), 3049–3057. https://doi.org/10.1021/jm2014666
Rueda, M., Totrov, M., & Abagyan, R. (2012). ALiBERO: evolving a team of complementary pocket conformations rather than a single leader. Journal of Chemical Information and Modeling, 52(10), 2705–2714. https://doi.org/10.1021/ci3001088
Orry, A. J. W., & Abagyan, R. (2012). Preparation and refinement of model protein-ligand complexes. Methods in Molecular Biology (Clifton, N.J.), 857, 351–373. https://doi.org/10.1007/978-1-61779-588-6_16
Neves, M. A. C., Yeager, M., & Abagyan, R. (2012). Unusual arginine formations in protein function and assembly: Rings, strings, and stacks. The Journal of Physical Chemistry. B, 116(23), 7006–7013. https://doi.org/10.1021/jp3009699
Neves, M. A. C., Totrov, M., & Abagyan, R. (2012). Docking and scoring with ICM: the benchmarking results and strategies for improvement. Journal of Computer-Aided Molecular Design, 26(6), 675–686. https://doi.org/10.1007/s10822-012-9547-0
Leung, C.-H., Zhong, H.-J., Yang, H., Cheng, Z., Chan, D. S.-H., Ma, V. P.-Y., Abagyan, R., Wong, C.-Y., & Ma, D.-L. (2012). A metal-based inhibitor of tumor necrosis factor-α. Angewandte Chemie (International Ed. in English), 51(36), 9010–9014. https://doi.org/10.1002/anie.201202937
Kufareva, I., Ilatovskiy, A. V., & Abagyan, R. (2012). Pocketome: An encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Research, 40(Database issue), D535-540. https://doi.org/10.1093/nar/gkr825
Kufareva, I., Chen, Y.-C., Ilatovskiy, A. V., & Abagyan, R. (2012). Compound activity prediction using models of binding pockets or ligand properties in 3D. Current Topics in Medicinal Chemistry, 12(17), 1869–1882. https://doi.org/10.2174/156802612804547335
Kufareva, I., & Abagyan, R. (2012). Methods of protein structure comparison. Methods in Molecular Biology (Clifton, N.J.), 857, 231–257. https://doi.org/10.1007/978-1-61779-588-6_10
Katritch, V., Rueda, M., & Abagyan, R. (2012). Ligand-guided receptor optimization. Methods in Molecular Biology (Clifton, N.J.), 857, 189–205. https://doi.org/10.1007/978-1-61779-588-6_8
Jarończyk, M., Wołosewicz, K., Gabrielsen, M., Nowak, G., Kufareva, I., Mazurek, A. P., Ravna, A. W., Abagyan, R., Bojarski, A. J., Sylte, I., & Chilmonczyk, Z. (2012). Synthesis, in vitro binding studies and docking of long-chain arylpiperazine nitroquipazine analogues, as potential serotonin transporter inhibitors. European Journal of Medicinal Chemistry, 49, 200–210. https://doi.org/10.1016/j.ejmech.2012.01.012
Gabrielsen, M., Kurczab, R., Ravna, A. W., Kufareva, I., Abagyan, R., Chilmonczyk, Z., Bojarski, A. J., & Sylte, I. (2012). Molecular mechanism of serotonin transporter inhibition elucidated by a new flexible docking protocol. European Journal of Medicinal Chemistry, 47(1), 24–37. https://doi.org/10.1016/j.ejmech.2011.09.056
Dong, M., Xu, X., Ball, A. M., Makhoul, J. A., Lam, P. C.-H., Pinon, D. I., Orry, A., Sexton, P. M., Abagyan, R., & Miller, L. J. (2012). Mapping spatial approximations between the amino terminus of secretin and each of the extracellular loops of its receptor using cysteine trapping. FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology, 26(12), 5092–5105. https://doi.org/10.1096/fj.12-212399
Chan, F.-Y., Neves, M. A. C., Sun, N., Tsang, M.-W., Leung, Y.-C., Chan, T.-H., Abagyan, R., & Wong, K.-Y. (2012). Validation of the AmpC β-lactamase binding site and identification of inhibitors with novel scaffolds. Journal of Chemical Information and Modeling, 52(5), 1367–1375. https://doi.org/10.1021/ci300068m
Cawston, E. E., Lam, P. C. H., Harikumar, K. G., Dong, M., Ball, A. M., Augustine, M. L., Akgün, E., Portoghese, P. S., Orry, A., Abagyan, R., Sexton, P. M., & Miller, L. J. (2012). Molecular basis for binding and subtype selectivity of 1,4-benzodiazepine antagonist ligands of the cholecystokinin receptor. The Journal of Biological Chemistry, 287(22), 18618–18635. https://doi.org/10.1074/jbc.M111.335646
Abagyan, R. (2012). Computational chemistry in 25 years. Journal of Computer-Aided Molecular Design, 26(1), 9–10. https://doi.org/10.1007/s10822-011-9516-z
Teplova, M., Malinina, L., Darnell, J. C., Song, J., Lu, M., Abagyan, R., Musunuru, K., Teplov, A., Burley, S. K., Darnell, R. B., & Patel, D. J. (2011). Protein-RNA and protein-protein recognition by dual KH1/2 domains of the neuronal splicing factor Nova-1. Structure (London, England : 1993), 19(7), 930–944. https://doi.org/10.1016/j.str.2011.05.002
Svobodová Vareková, R., Geidl, S., Ionescu, C.-M., Skrehota, O., Kudera, M., Sehnal, D., Bouchal, T., Abagyan, R., Huber, H. J., & Koca, J. (2011). Predicting pK(a) values of substituted phenols from atomic charges: Comparison of different quantum mechanical methods and charge distribution schemes. Journal of Chemical Information and Modeling, 51(8), 1795–1806. https://doi.org/10.1021/ci200133w
Shimamura, T., Shiroishi, M., Weyand, S., Tsujimoto, H., Winter, G., Katritch, V., Abagyan, R., Cherezov, V., Liu, W., Han, G. W., Kobayashi, T., Stevens, R. C., & Iwata, S. (2011). Structure of the human histamine H1 receptor complex with doxepin. Nature, 475(7354), 65–70. https://doi.org/10.1038/nature10236
Miller, L. J., Chen, Q., Lam, P. C.-H., Pinon, D. I., Sexton, P. M., Abagyan, R., & Dong, M. (2011). Refinement of glucagon-like peptide 1 docking to its intact receptor using mid-region photolabile probes and molecular modeling. The Journal of Biological Chemistry, 286(18), 15895–15907. https://doi.org/10.1074/jbc.M110.217901
Lin, C., Ear, J., Pavlova, Y., Mittal, Y., Kufareva, I., Ghassemian, M., Abagyan, R., Garcia-Marcos, M., & Ghosh, P. (2011). Tyrosine phosphorylation of the Gα-interacting protein GIV promotes activation of phosphoinositide 3-kinase during cell migration. Science Signaling, 4(192), ra64. https://doi.org/10.1126/scisignal.2002049
Leung, C.-H., Chan, D. S.-H., Yang, H., Abagyan, R., Lee, S. M.-Y., Zhu, G.-Y., Fong, W.-F., & Ma, D.-L. (2011). A natural product-like inhibitor of NEDD8-activating enzyme. Chemical Communications (Cambridge, England), 47(9), 2511–2513. https://doi.org/10.1039/c0cc04927a
Lee, W. H., Yue, W. W., Raush, E., Totrov, M., Abagyan, R., Oppermann, U., & Marsden, B. D. (2011). Interactive JIMD articles using the iSee concept: Turning a new page on structural biology data. Journal of Inherited Metabolic Disease, 34(3), 565–567. https://doi.org/10.1007/s10545-011-9334-4
Kufareva, I., Rueda, M., Katritch, V., Stevens, R. C., & Abagyan, R. (2011). Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure (London, England : 1993), 19(8), 1108–1126. https://doi.org/10.1016/j.str.2011.05.012
Katritch, V., Kufareva, I., & Abagyan, R. (2011). Structure based prediction of subtype-selectivity for adenosine receptor antagonists. Neuropharmacology, 60(1), 108–115. https://doi.org/10.1016/j.neuropharm.2010.07.009
Katritch, V., & Abagyan, R. (2011). GPCR agonist binding revealed by modeling and crystallography. Trends in Pharmacological Sciences, 32(11), 637–643. https://doi.org/10.1016/j.tips.2011.08.001
Dong, M., Lam, P. C.-H., Pinon, D. I., Hosohata, K., Orry, A., Sexton, P. M., Abagyan, R., & Miller, L. J. (2011). Molecular basis of secretin docking to its intact receptor using multiple photolabile probes distributed throughout the pharmacophore. The Journal of Biological Chemistry, 286(27), 23888–23899. https://doi.org/10.1074/jbc.M111.245969
Bottegoni, G., Rocchia, W., Rueda, M., Abagyan, R., & Cavalli, A. (2011). Systematic exploitation of multiple receptor conformations for virtual ligand screening. PloS One, 6(5), e18845. https://doi.org/10.1371/journal.pone.0018845
Bordner, A. J., Zorman, B., & Abagyan, R. (2011). Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model. Journal of Computer-Aided Molecular Design, 25(10), 895–911. https://doi.org/10.1007/s10822-011-9470-9
Arnautova, Y. A., Abagyan, R. A., & Totrov, M. (2011). Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling. Proteins, 79(2), 477–498. https://doi.org/10.1002/prot.22896
Wu, B., Chien, E. Y. T., Mol, C. D., Fenalti, G., Liu, W., Katritch, V., Abagyan, R., Brooun, A., Wells, P., Bi, F. C., Hamel, D. J., Kuhn, P., Handel, T. M., Cherezov, V., & Stevens, R. C. (2010). Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science (New York, N.Y.), 330(6007), 1066–1071. https://doi.org/10.1126/science.1194396
Wacker, D., Fenalti, G., Brown, M. A., Katritch, V., Abagyan, R., Cherezov, V., & Stevens, R. C. (2010). Conserved binding mode of human beta2 adrenergic receptor inverse agonists and antagonist revealed by X-ray crystallography. Journal of the American Chemical Society, 132(33), 11443–11445. https://doi.org/10.1021/ja105108q
Totrov, M., Jiang, X., Kong, X.-P., Cohen, S., Krachmarov, C., Salomon, A., Williams, C., Seaman, M. S., Abagyan, R., Cardozo, T., Gorny, M. K., Wang, S., Lu, S., Pinter, A., & Zolla-Pazner, S. (2010). Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold. Virology, 405(2), 513–523. https://doi.org/10.1016/j.virol.2010.06.027
Rueda, M., Katritch, V., Raush, E., & Abagyan, R. (2010). SimiCon: A web tool for protein-ligand model comparison through calculation of equivalent atomic contacts. Bioinformatics (Oxford, England), 26(21), 2784–2785. https://doi.org/10.1093/bioinformatics/btq504
Rueda, M., Bottegoni, G., & Abagyan, R. (2010). Recipes for the selection of experimental protein conformations for virtual screening. Journal of Chemical Information and Modeling, 50(1), 186–193. https://doi.org/10.1021/ci9003943
Park, S.-J., Kufareva, I., & Abagyan, R. (2010). Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles. Journal of Computer-Aided Molecular Design, 24(5), 459–471. https://doi.org/10.1007/s10822-010-9362-4
Odell, L. R., Howan, D., Gordon, C. P., Robertson, M. J., Chau, N., Mariana, A., Whiting, A. E., Abagyan, R., Daniel, J. A., Gorgani, N. N., Robinson, P. J., & McCluskey, A. (2010). The pthaladyns: GTP competitive inhibitors of dynamin I and II GTPase derived from virtual screening. Journal of Medicinal Chemistry, 53(14), 5267–5280. https://doi.org/10.1021/jm100442u
Katritch, V., Rueda, M., Lam, P. C.-H., Yeager, M., & Abagyan, R. (2010). GPCR 3D homology models for ligand screening: Lessons learned from blind predictions of adenosine A2a receptor complex. Proteins, 78(1), 197–211. https://doi.org/10.1002/prot.22507
Katritch, V., Jaakola, V.-P., Lane, J. R., Lin, J., Ijzerman, A. P., Yeager, M., Kufareva, I., Stevens, R. C., & Abagyan, R. (2010). Structure-based discovery of novel chemotypes for adenosine A(2A) receptor antagonists. Journal of Medicinal Chemistry, 53(4), 1799–1809. https://doi.org/10.1021/jm901647p
Grigoryan, A. V., Kufareva, I., Totrov, M., & Abagyan, R. A. (2010). Spatial chemical distance based on atomic property fields. Journal of Computer-Aided Molecular Design, 24(3), 173–182. https://doi.org/10.1007/s10822-009-9316-x
Dong, M., Lam, P. C.-H., Pinon, D. I., Orry, A., Sexton, P. M., Abagyan, R., & Miller, L. J. (2010). Secretin occupies a single protomer of the homodimeric secretin receptor complex: Insights from photoaffinity labeling studies using dual sites of covalent attachment. The Journal of Biological Chemistry, 285(13), 9919–9931. https://doi.org/10.1074/jbc.M109.089730
Chow, K. H.-M., Sun, R. W.-Y., Lam, J. B. B., Li, C. K.-L., Xu, A., Ma, D.-L., Abagyan, R., Wang, Y., & Che, C.-M. (2010). A gold(III) porphyrin complex with antitumor properties targets the Wnt/beta-catenin pathway. Cancer Research, 70(1), 329–337. https://doi.org/10.1158/0008-5472.CAN-09-3324
Cheltsov, A. V., Aoyagi, M., Aleshin, A., Yu, E. C.-W., Gilliland, T., Zhai, D., Bobkov, A. A., Reed, J. C., Liddington, R. C., & Abagyan, R. (2010). Vaccinia virus virulence factor N1L is a novel promising target for antiviral therapeutic intervention. Journal of Medicinal Chemistry, 53(10), 3899–3906. https://doi.org/10.1021/jm901446n
Chan, D. S.-H., Lee, H.-M., Yang, F., Che, C.-M., Wong, C. C. L., Abagyan, R., Leung, C.-H., & Ma, D.-L. (2010). Structure-based discovery of natural-product-like TNF-α inhibitors. Angewandte Chemie (International Ed. in English), 49(16), 2860–2864. https://doi.org/10.1002/anie.200907360
Bowers, E. M., Yan, G., Mukherjee, C., Orry, A., Wang, L., Holbert, M. A., Crump, N. T., Hazzalin, C. A., Liszczak, G., Yuan, H., Larocca, C., Saldanha, S. A., Abagyan, R., Sun, Y., Meyers, D. J., Marmorstein, R., Mahadevan, L. C., Alani, R. M., & Cole, P. A. (2010). Virtual ligand screening of the p300/CBP histone acetyltransferase: Identification of a selective small molecule inhibitor. Chemistry & Biology, 17(5), 471–482. https://doi.org/10.1016/j.chembiol.2010.03.006
Wu, Y.-W., Goody, R. S., Abagyan, R., & Alexandrov, K. (2009). Structure of the disordered C terminus of Rab7 GTPase induced by binding to the Rab geranylgeranyl transferase catalytic complex reveals the mechanism of Rab prenylation. The Journal of Biological Chemistry, 284(19), 13185–13192. https://doi.org/10.1074/jbc.M900579200
Wu, P., Ma, D.-L., Leung, C.-H., Yan, S.-C., Zhu, N., Abagyan, R., & Che, C.-M. (2009). Stabilization of G-quadruplex DNA with platinum(II) Schiff base complexes: Luminescent probe and down-regulation of c-myc oncogene expression. Chemistry (Weinheim an Der Bergstrasse, Germany), 15(47), 13008–13021. https://doi.org/10.1002/chem.200901943
Simms, J., Hall, N. E., Lam, P. H. C., Miller, L. J., Christopoulos, A., Abagyan, R., & Sexton, P. M. (2009). Homology modeling of GPCRs. Methods in Molecular Biology (Clifton, N.J.), 552, 97–113. https://doi.org/10.1007/978-1-60327-317-6_7
Rueda, M., Bottegoni, G., & Abagyan, R. (2009). Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes. Journal of Chemical Information and Modeling, 49(3), 716–725. https://doi.org/10.1021/ci8003732
Reynolds, K. A., Katritch, V., & Abagyan, R. (2009). Identifying conformational changes of the beta(2) adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators. Journal of Computer-Aided Molecular Design, 23(5), 273–288. https://doi.org/10.1007/s10822-008-9257-9
Raush, E., Totrov, M., Marsden, B. D., & Abagyan, R. (2009). A new method for publishing three-dimensional content. PloS One, 4(10), e7394. https://doi.org/10.1371/journal.pone.0007394
Nicola, G., & Abagyan, R. (2009). Structure-based approaches to antibiotic drug discovery. Current Protocols in Microbiology, Chapter 17, Unit17.2. https://doi.org/10.1002/9780471729259.mc1702s12
Lee, W. H., Atienza-Herrero, J., Abagyan, R., & Marsden, B. D. (2009). SGC--structural biology and human health: A new approach to publishing structural biology results. PloS One, 4(10), e7675. https://doi.org/10.1371/journal.pone.0007675
Katritch, V., Reynolds, K. A., Cherezov, V., Hanson, M. A., Roth, C. B., Yeager, M., & Abagyan, R. (2009). Analysis of full and partial agonists binding to beta2-adrenergic receptor suggests a role of transmembrane helix V in agonist-specific conformational changes. Journal of Molecular Recognition : JMR, 22(4), 307–318. https://doi.org/10.1002/jmr.949
Garzon, J. I., Lopéz-Blanco, J. R., Pons, C., Kovacs, J., Abagyan, R., Fernandez-Recio, J., & Chacon, P. (2009). FRODOCK: a new approach for fast rotational protein-protein docking. Bioinformatics (Oxford, England), 25(19), 2544–2551. https://doi.org/10.1093/bioinformatics/btp447
Gao, F., Harikumar, K. G., Dong, M., Lam, P. C.-H., Sexton, P. M., Christopoulos, A., Bordner, A., Abagyan, R., & Miller, L. J. (2009). Functional importance of a structurally distinct homodimeric complex of the family B G protein-coupled secretin receptor. Molecular Pharmacology, 76(2), 264–274. https://doi.org/10.1124/mol.109.055756
Dong, M., Lam, P. C.-H., Pinon, D. I., Abagyan, R., & Miller, L. J. (2009). Elucidation of the molecular basis of cholecystokinin Peptide docking to its receptor using site-specific intrinsic photoaffinity labeling and molecular modeling. Biochemistry, 48(23), 5303–5312. https://doi.org/10.1021/bi9004705
Bottegoni, G., Kufareva, I., Totrov, M., & Abagyan, R. (2009). Four-dimensional docking: A fast and accurate account of discrete receptor flexibility in ligand docking. Journal of Medicinal Chemistry, 52(2), 397–406. https://doi.org/10.1021/jm8009958
Bisson, W. H., Koch, D. C., O’Donnell, E. F., Khalil, S. M., Kerkvliet, N. I., Tanguay, R. L., Abagyan, R., & Kolluri, S. K. (2009). Modeling of the aryl hydrocarbon receptor (AhR) ligand binding domain and its utility in virtual ligand screening to predict new AhR ligands. Journal of Medicinal Chemistry, 52(18), 5635–5641. https://doi.org/10.1021/jm900199u
Abagyan, R., & Kufareva, I. (2009). The flexible pocketome engine for structural chemogenomics. Methods in Molecular Biology (Clifton, N.J.), 575, 249–279. https://doi.org/10.1007/978-1-60761-274-2_11
Totrov, M., & Abagyan, R. (2008). Flexible ligand docking to multiple receptor conformations: A practical alternative. Current Opinion in Structural Biology, 18(2), 178–184. https://doi.org/10.1016/j.sbi.2008.01.004
Nicola, G., Smith, C. A., & Abagyan, R. (2008). New method for the assessment of all drug-like pockets across a structural genome. Journal of Computational Biology : A Journal of Computational Molecular Cell Biology, 15(3), 231–240. https://doi.org/10.1089/cmb.2007.0178
Medina, M., Abagyan, R., Gómez-Moreno, C., & Fernandez-Recio, J. (2008). Docking analysis of transient complexes: Interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin. Proteins, 72(3), 848–862. https://doi.org/10.1002/prot.21979
Ma, D.-L., Lai, T.-S., Chan, F.-Y., Chung, W.-H., Abagyan, R., Leung, Y.-C., & Wong, K.-Y. (2008). Discovery of a drug-like G-quadruplex binding ligand by high-throughput docking. ChemMedChem, 3(6), 881–884. https://doi.org/10.1002/cmdc.200700342
Lee, H. S., Choi, J., Kufareva, I., Abagyan, R., Filikov, A., Yang, Y., & Yoon, S. (2008). Optimization of high throughput virtual screening by combining shape-matching and docking methods. Journal of Chemical Information and Modeling, 48(3), 489–497. https://doi.org/10.1021/ci700376c
Kufareva, I., & Abagyan, R. (2008). Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. Journal of Medicinal Chemistry, 51(24), 7921–7932. https://doi.org/10.1021/jm8010299
Kovacs, J. A., Yeager, M., & Abagyan, R. (2008). Damped-dynamics flexible fitting. Biophysical Journal, 95(7), 3192–3207. https://doi.org/10.1529/biophysj.108.132357
Dong, M., Lam, P. C.-H., Pinon, D. I., Sexton, P. M., Abagyan, R., & Miller, L. J. (2008). Spatial approximation between secretin residue five and the third extracellular loop of its receptor provides new insight into the molecular basis of natural agonist binding. Molecular Pharmacology, 74(2), 413–422. https://doi.org/10.1124/mol.108.047209
Cavasotto, C. N., Orry, A. J. W., Murgolo, N. J., Czarniecki, M. F., Kocsi, S. A., Hawes, B. E., O’Neill, K. A., Hine, H., Burton, M. S., Voigt, J. H., Abagyan, R. A., Bayne, M. L., & Monsma, F. J. J. (2008). Discovery of novel chemotypes to a G-protein-coupled receptor through ligand-steered homology modeling and structure-based virtual screening. Journal of Medicinal Chemistry, 51(3), 581–588. https://doi.org/10.1021/jm070759m
Bottegoni, G., Kufareva, I., Totrov, M., & Abagyan, R. (2008). A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). Journal of Computer-Aided Molecular Design, 22(5), 311–325. https://doi.org/10.1007/s10822-008-9188-5
Bisson, W. H., Abagyan, R., & Cavasotto, C. N. (2008). Molecular basis of agonicity and antagonicity in the androgen receptor studied by molecular dynamics simulations. Journal of Molecular Graphics & Modelling, 27(4), 452–458. https://doi.org/10.1016/j.jmgm.2008.08.001
Szewczuk, L. M., Saldanha, S. A., Ganguly, S., Bowers, E. M., Javoroncov, M., Karanam, B., Culhane, J. C., Holbert, M. A., Klein, D. C., Abagyan, R., & Cole, P. A. (2007). De novo discovery of serotonin N-acetyltransferase inhibitors. Journal of Medicinal Chemistry, 50(22), 5330–5338. https://doi.org/10.1021/jm0706463
Raduner, S., Bisson, W., Abagyan, R., Altmann, K.-H., & Gertsch, J. (2007). Self-assembling cannabinomimetics: Supramolecular structures of N-alkyl amides. Journal of Natural Products, 70(6), 1010–1015. https://doi.org/10.1021/np060598+
Outeiro, T. F., Kontopoulos, E., Altmann, S. M., Kufareva, I., Strathearn, K. E., Amore, A. M., Volk, C. B., Maxwell, M. M., Rochet, J.-C., McLean, P. J., Young, A. B., Abagyan, R., Feany, M. B., Hyman, B. T., & Kazantsev, A. G. (2007). Sirtuin 2 inhibitors rescue alpha-synuclein-mediated toxicity in models of Parkinson’s disease. Science (New York, N.Y.), 317(5837), 516–519. https://doi.org/10.1126/science.1143780
Nicola, G., Smith, C. A., Lucumi, E., Kuo, M. R., Karagyozov, L., Fidock, D. A., Sacchettini, J. C., & Abagyan, R. (2007). Discovery of novel inhibitors targeting enoyl-acyl carrier protein reductase in Plasmodium falciparum by structure-based virtual screening. Biochemical and Biophysical Research Communications, 358(3), 686–691. https://doi.org/10.1016/j.bbrc.2007.04.113
Mallya, M., Phillips, R. L., Saldanha, S. A., Gooptu, B., Brown, S. C. L., Termine, D. J., Shirvani, A. M., Wu, Y., Sifers, R. N., Abagyan, R., & Lomas, D. A. (2007). Small molecules block the polymerization of Z alpha1-antitrypsin and increase the clearance of intracellular aggregates. Journal of Medicinal Chemistry, 50(22), 5357–5363. https://doi.org/10.1021/jm070687z
Kufareva, I., Budagyan, L., Raush, E., Totrov, M., & Abagyan, R. (2007). PIER: protein interface recognition for structural proteomics. Proteins, 67(2), 400–417. https://doi.org/10.1002/prot.21233
Kovacs, J. A., Yeager, M., & Abagyan, R. (2007). Computational prediction of atomic structures of helical membrane proteins aided by EM maps. Biophysical Journal, 93(6), 1950–1959. https://doi.org/10.1529/biophysj.106.102137
Kovacs, J. A., Baker, K. A., Altenberg, G. A., Abagyan, R., & Yeager, M. (2007). Molecular modeling and mutagenesis of gap junction channels. Progress in Biophysics and Molecular Biology, 94(1–2), 15–28. https://doi.org/10.1016/j.pbiomolbio.2007.03.013
Katritch, V., Byrd, C. M., Tseitin, V., Dai, D., Raush, E., Totrov, M., Abagyan, R., Jordan, R., & Hruby, D. E. (2007). Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches. Journal of Computer-Aided Molecular Design, 21(10–11), 549–558. https://doi.org/10.1007/s10822-007-9138-7
Hayashi, T., Mo, J.-H., Gong, X., Rossetto, C., Jang, A., Beck, L., Elliott, G. I., Kufareva, I., Abagyan, R., Broide, D. H., Lee, J., & Raz, E. (2007). 3-Hydroxyanthranilic acid inhibits PDK1 activation and suppresses experimental asthma by inducing T cell apoptosis. Proceedings of the National Academy of Sciences of the United States of America, 104(47), 18619–18624. https://doi.org/10.1073/pnas.0709261104
Harikumar, K. G., Lam, P. C.-H., Dong, M., Sexton, P. M., Abagyan, R., & Miller, L. J. (2007). Fluorescence resonance energy transfer analysis of secretin docking to its receptor: Mapping distances between residues distributed throughout the ligand pharmacophore and distinct receptor residues. The Journal of Biological Chemistry, 282(45), 32834–32843. https://doi.org/10.1074/jbc.M704563200
Garzón, J. I., Kovacs, J., Abagyan, R., & Chacón, P. (2007). DFprot: A webtool for predicting local chain deformability. Bioinformatics (Oxford, England), 23(7), 901–902. https://doi.org/10.1093/bioinformatics/btm014
Garzón, J. I., Kovacs, J., Abagyan, R., & Chacón, P. (2007). ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage. Bioinformatics (Oxford, England), 23(4), 427–433. https://doi.org/10.1093/bioinformatics/btl625
Dong, M., Lam, P. C.-H., Gao, F., Hosohata, K., Pinon, D. I., Sexton, P. M., Abagyan, R., & Miller, L. J. (2007). Molecular approximations between residues 21 and 23 of secretin and its receptor: Development of a model for peptide docking with the amino terminus of the secretin receptor. Molecular Pharmacology, 72(2), 280–290. https://doi.org/10.1124/mol.107.035402
Dong, M., Ding, X.-Q., Thomas, S. E., Gao, F., Lam, P. C.-H., Abagyan, R., & Miller, L. J. (2007). Role of lysine187 within the second extracellular loop of the type A cholecystokinin receptor in agonist-induced activation. Use of complementary charge-reversal mutagenesis to define a functionally important interdomain interaction. Biochemistry, 46(15), 4522–4531. https://doi.org/10.1021/bi0622468
Chrencik, J. E., Brooun, A., Recht, M. I., Nicola, G., Davis, L. K., Abagyan, R., Widmer, H., Pasquale, E. B., & Kuhn, P. (2007). Three-dimensional structure of the EphB2 receptor in complex with an antagonistic peptide reveals a novel mode of inhibition. The Journal of Biological Chemistry, 282(50), 36505–36513. https://doi.org/10.1074/jbc.M706340200
Bisson, W. H., Cheltsov, A. V., Bruey-Sedano, N., Lin, B., Chen, J., Goldberger, N., May, L. T., Christopoulos, A., Dalton, J. T., Sexton, P. M., Zhang, X.-K., & Abagyan, R. (2007). Discovery of antiandrogen activity of nonsteroidal scaffolds of marketed drugs. Proceedings of the National Academy of Sciences of the United States of America, 104(29), 11927–11932. https://doi.org/10.1073/pnas.0609752104
Smith, C. A., Want, E. J., O’Maille, G., Abagyan, R., & Siuzdak, G. (2006). XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Analytical Chemistry, 78(3), 779–787. https://doi.org/10.1021/ac051437y
Saldanha, S. A., Kaler, G., Cottam, H. B., Abagyan, R., & Taylor, S. S. (2006). Assay principle for modulators of protein-protein interactions and its application to non-ATP-competitive ligands targeting protein kinase A. Analytical Chemistry, 78(24), 8265–8272. https://doi.org/10.1021/ac061104g
Orry, A. J. W., Abagyan, R. A., & Cavasotto, C. N. (2006). Structure-based development of target-specific compound libraries. Drug Discovery Today, 11(5–6), 261–266. https://doi.org/10.1016/S1359-6446(05)03717-7
Malinina, L., Malakhova, M. L., Kanack, A. T., Lu, M., Abagyan, R., Brown, R. E., & Patel, D. J. (2006). The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure. PLoS Biology, 4(11), e362. https://doi.org/10.1371/journal.pbio.0040362
Huang, Y., Qiao, F., Abagyan, R., Hazard, S., & Tomlinson, S. (2006). Defining the CD59-C9 binding interaction. The Journal of Biological Chemistry, 281(37), 27398–27404. https://doi.org/10.1074/jbc.M603690200
Cavasotto, C. N., Ortiz, M. A., Abagyan, R. A., & Piedrafita, F. J. (2006). In silico identification of novel EGFR inhibitors with antiproliferative activity against cancer cells. Bioorganic & Medicinal Chemistry Letters, 16(7), 1969–1974. https://doi.org/10.1016/j.bmcl.2005.12.067
Budagyan, L., & Abagyan, R. (2006). Weighted quality estimates in machine learning. Bioinformatics (Oxford, England), 22(21), 2597–2603. https://doi.org/10.1093/bioinformatics/btl458
Bordner, A. J., & Abagyan, R. (2006). Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes. Proteins, 63(3), 512–526. https://doi.org/10.1002/prot.20831
Altmann, S. M., Muryshev, A., Fossale, E., Maxwell, M. M., Norflus, F. N., Fox, J., Hersch, S. M., Young, A. B., MacDonald, M. E., Abagyan, R., & Kazantsev, A. G. (2006). Discovery of bioactive small-molecule inhibitor of poly adp-ribose polymerase: Implications for energy-deficient cells. Chemistry & Biology, 13(7), 765–770. https://doi.org/10.1016/j.chembiol.2006.05.012
Abagyan, R., Lee, W. H., Raush, E., Budagyan, L., Totrov, M., Sundstrom, M., & Marsden, B. D. (2006). Disseminating structural genomics data to the public: From a data dump to an animated story. Trends in Biochemical Sciences, 31(2), 76–78. https://doi.org/10.1016/j.tibs.2005.12.006
Tetko, I. V., Abagyan, R., & Oprea, T. I. (2005). Surrogate data—A secure way to share corporate data. Journal of Computer-Aided Molecular Design, 19(9–10), 749–764. https://doi.org/10.1007/s10822-005-9013-3
Smith, C. A., O’Maille, G., Want, E. J., Qin, C., Trauger, S. A., Brandon, T. R., Custodio, D. E., Abagyan, R., & Siuzdak, G. (2005). METLIN: a metabolite mass spectral database. Therapeutic Drug Monitoring, 27(6), 747–751. https://doi.org/10.1097/01.ftd.0000179845.53213.39
Huang, Y., Smith, C. A., Song, H., Morgan, B. P., Abagyan, R., & Tomlinson, S. (2005). Insights into the human CD59 complement binding interface toward engineering new therapeutics. The Journal of Biological Chemistry, 280(40), 34073–34079. https://doi.org/10.1074/jbc.M504922200
Hill, T., Odell, L. R., Edwards, J. K., Graham, M. E., McGeachie, A. B., Rusak, J., Quan, A., Abagyan, R., Scott, J. L., Robinson, P. J., & McCluskey, A. (2005). Small molecule inhibitors of dynamin I GTPase activity: Development of dimeric tyrphostins. Journal of Medicinal Chemistry, 48(24), 7781–7788. https://doi.org/10.1021/jm040208l
Forino, M., Johnson, S., Wong, T. Y., Rozanov, D. V., Savinov, A. Y., Li, W., Fattorusso, R., Becattini, B., Orry, A. J., Jung, D., Abagyan, R. A., Smith, J. W., Alibek, K., Liddington, R. C., Strongin, A. Y., & Pellecchia, M. (2005). Efficient synthetic inhibitors of anthrax lethal factor. Proceedings of the National Academy of Sciences of the United States of America, 102(27), 9499–9504. https://doi.org/10.1073/pnas.0502733102
Fernandez-Recio, J., Totrov, M., Skorodumov, C., & Abagyan, R. (2005). Optimal docking area: A new method for predicting protein-protein interaction sites. Proteins, 58(1), 134–143. https://doi.org/10.1002/prot.20285
Fernández-Recio, J., Abagyan, R., & Totrov, M. (2005). Improving CAPRI predictions: Optimized desolvation for rigid-body docking. Proteins, 60(2), 308–313. https://doi.org/10.1002/prot.20575
Cavasotto, C. N., Kovacs, J. A., & Abagyan, R. A. (2005). Representing receptor flexibility in ligand docking through relevant normal modes. Journal of the American Chemical Society, 127(26), 9632–9640. https://doi.org/10.1021/ja042260c
Cardozo, T., & Abagyan, R. (2005). Druggability of SCF ubiquitin ligase-protein interfaces. Methods in Enzymology, 399, 634–653. https://doi.org/10.1016/S0076-6879(05)99042-3
Bordner, A. J., & Abagyan, R. (2005). Statistical analysis and prediction of protein-protein interfaces. Proteins, 60(3), 353–366. https://doi.org/10.1002/prot.20433
Bordner, A. J., & Abagyan, R. (2005). REVCOM: a robust Bayesian method for evolutionary rate estimation. Bioinformatics (Oxford, England), 21(10), 2315–2321. https://doi.org/10.1093/bioinformatics/bti347
An, J., Totrov, M., & Abagyan, R. (2005). Pocketome via comprehensive identification and classification of ligand binding envelopes. Molecular & Cellular Proteomics : MCP, 4(6), 752–761. https://doi.org/10.1074/mcp.M400159-MCP200
Marsden, B., & Abagyan, R. (2004). SAD--a normalized structural alignment database: Improving sequence-structure alignments. Bioinformatics (Oxford, England), 20(15), 2333–2344. https://doi.org/10.1093/bioinformatics/bth244
Kovacs, J. A., Chacón, P., & Abagyan, R. (2004). Predictions of protein flexibility: First-order measures. Proteins, 56(4), 661–668. https://doi.org/10.1002/prot.20151
Hill, T. A., Odell, L. R., Quan, A., Abagyan, R., Ferguson, G., Robinson, P. J., & McCluskey, A. (2004). Long chain amines and long chain ammonium salts as novel inhibitors of dynamin GTPase activity. Bioorganic & Medicinal Chemistry Letters, 14(12), 3275–3278. https://doi.org/10.1016/j.bmcl.2004.03.096
Fernández-Recio, J., Totrov, M., & Abagyan, R. (2004). Identification of protein-protein interaction sites from docking energy landscapes. Journal of Molecular Biology, 335(3), 843–865. https://doi.org/10.1016/j.jmb.2003.10.069
Cavasotto, C. N., Liu, G., James, S. Y., Hobbs, P. D., Peterson, V. J., Bhattacharya, A. A., Kolluri, S. K., Zhang, X., Leid, M., Abagyan, R., Liddington, R. C., & Dawson, M. I. (2004). Determinants of retinoid X receptor transcriptional antagonism. Journal of Medicinal Chemistry, 47(18), 4360–4372. https://doi.org/10.1021/jm030651g
Cavasotto, C. N., & Abagyan, R. A. (2004). Protein flexibility in ligand docking and virtual screening to protein kinases. Journal of Molecular Biology, 337(1), 209–225. https://doi.org/10.1016/j.jmb.2004.01.003
Bordner, A. J., & Abagyan, R. A. (2004). Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations. Proteins, 57(2), 400–413. https://doi.org/10.1002/prot.20185
An, J., Totrov, M., & Abagyan, R. (2004). Comprehensive identification of “druggable” protein ligand binding sites. Genome Informatics. International Conference on Genome Informatics, 15(2), 31–41. PMID: 15706489
Zhou, Y., & Abagyan, R. (2003). Algorithms for high-density oligonucleotide array. Current Opinion in Drug Discovery & Development, 6(3), 339–345.
Schapira, M., Raaka, B. M., Das, S., Fan, L., Totrov, M., Zhou, Z., Wilson, S. R., Abagyan, R., & Samuels, H. H. (2003). Discovery of diverse thyroid hormone receptor antagonists by high-throughput docking. Proceedings of the National Academy of Sciences of the United States of America, 100(12), 7354–7359. https://doi.org/10.1073/pnas.1131854100
Schapira, M., Abagyan, R., & Totrov, M. (2003). Nuclear hormone receptor targeted virtual screening. Journal of Medicinal Chemistry, 46(14), 3045–3059. https://doi.org/10.1021/jm0300173
Katritch, V., Totrov, M., & Abagyan, R. (2003). ICFF: a new method to incorporate implicit flexibility into an internal coordinate force field. Journal of Computational Chemistry, 24(2), 254–265. https://doi.org/10.1002/jcc.10091
Fernández-Recio, J., Totrov, M., & Abagyan, R. (2003). ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins, 52(1), 113–117. https://doi.org/10.1002/prot.10383
Eneqvist, T., Lundberg, E., Nilsson, L., Abagyan, R., & Sauer-Eriksson, A. E. (2003). The transthyretin-related protein family. European Journal of Biochemistry, 270(3), 518–532. https://doi.org/10.1046/j.1432-1033.2003.03408.x
Cavasotto, C. N., Orry, A. J. W., & Abagyan, R. A. (2003). Structure-based identification of binding sites, native ligands and potential inhibitors for G-protein coupled receptors. Proteins, 51(3), 423–433. https://doi.org/10.1002/prot.10362
Bursulaya, B. D., Totrov, M., Abagyan, R., & Brooks, C. L. 3rd. (2003). Comparative study of several algorithms for flexible ligand docking. Journal of Computer-Aided Molecular Design, 17(11), 755–763. https://doi.org/10.1023/b:jcam.0000017496.76572.6f
Zhou, Y., & Abagyan, R. (2002). Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis. BMC Bioinformatics, 3, 3. https://doi.org/10.1186/1471-2105-3-3
Volkman, S. K., Hartl, D. L., Wirth, D. F., Nielsen, K. M., Choi, M., Batalov, S., Zhou, Y., Plouffe, D., Le Roch, K. G., Abagyan, R., & Winzeler, E. A. (2002). Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum. Science (New York, N.Y.), 298(5591), 216–218. https://doi.org/10.1126/science.1075642
Schapira, M., Abagyan, R., & Totrov, M. (2002). Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine. BMC Structural Biology, 2, 1. https://doi.org/10.1186/1472-6807-2-1
Fernández-Recio, J., Totrov, M., & Abagyan, R. (2002). Soft protein-protein docking in internal coordinates. Protein Science : A Publication of the Protein Society, 11(2), 280–291. https://doi.org/10.1110/ps.19202
Fernandez-Recio, J., Totrov, M., & Abagyan, R. (2002). Screened charge electrostatic model in protein-protein docking simulations. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 552–563. https://doi.org/10.1142/9789812799623_0052
Brive, L., & Abagyan, R. (2002). Computational structural proteomics. Ernst Schering Research Foundation Workshop, 38, 149–166. https://doi.org/10.1007/978-3-662-04747-7_8
Totrov, M., & Abagyan, R. (2001). Rapid boundary element solvation electrostatics calculations in folding simulations: Successful folding of a 23-residue peptide. Biopolymers, 60(2), 124–133. https://doi.org/10.1002/1097-0282(2001)60:2<124::AID-BIP1008>3.0.CO;2-S
Schapira, M., Raaka, B. M., Samuels, H. H., & Abagyan, R. (2001). In silico discovery of novel retinoic acid receptor agonist structures. BMC Structural Biology, 1, 1. https://doi.org/10.1186/1472-6807-1-1
Norledge, B. V., Lambeir, A. M., Abagyan, R. A., Rottmann, A., Fernandez, A. M., Filimonov, V. V., Peter, M. G., & Wierenga, R. K. (2001). Modeling, mutagenesis, and structural studies on the fully conserved phosphate-binding loop (loop 8) of triosephosphate isomerase: Toward a new substrate specificity. Proteins, 42(3), 383–389. https://doi.org/10.1002/1097-0134(20010215)42:3<383::aid-prot80>3.0.co;2-g
Abagyan, R., & Totrov, M. (2001). High-throughput docking for lead generation. Current Opinion in Chemical Biology, 5(4), 375–382. https://doi.org/10.1016/s1367-5931(00)00217-9
Tomko, R. P., Johansson, C. B., Totrov, M., Abagyan, R., Frisén, J., & Philipson, L. (2000). Expression of the adenovirus receptor and its interaction with the fiber knob. Experimental Cell Research, 255(1), 47–55. https://doi.org/10.1006/excr.1999.4761
Schapira, M., Raaka, B. M., Samuels, H. H., & Abagyan, R. (2000). Rational discovery of novel nuclear hormone receptor antagonists. Proceedings of the National Academy of Sciences of the United States of America, 97(3), 1008–1013. https://doi.org/10.1073/pnas.97.3.1008
Kelly, P. D., Chu, F., Woods, I. G., Ngo-Hazelett, P., Cardozo, T., Huang, H., Kimm, F., Liao, L., Yan, Y. L., Zhou, Y., Johnson, S. L., Abagyan, R., Schier, A. F., Postlethwait, J. H., & Talbot, W. S. (2000). Genetic linkage mapping of zebrafish genes and ESTs. Genome Research, 10(4), 558–567. https://doi.org/10.1101/gr.10.4.558
Jin, E., Katritch, V., Olson, W. K., Kharatisvili, M., Abagyan, R., & Pilch, D. S. (2000). Aminoglycoside binding in the major groove of duplex RNA: the thermodynamic and electrostatic forces that govern recognition. Journal of Molecular Biology, 298(1), 95–110. https://doi.org/10.1006/jmbi.2000.3639
Gantt, S., Persson, C., Rose, K., Birkett, A. J., Abagyan, R., & Nussenzweig, V. (2000). Antibodies against thrombospondin-related anonymous protein do not inhibit Plasmodium sporozoite infectivity in vivo. Infection and Immunity, 68(6), 3667–3673. https://doi.org/10.1128/IAI.68.6.3667-3673.2000
Filikov, A. V., Mohan, V., Vickers, T. A., Griffey, R. H., Cook, P. D., Abagyan, R. A., & James, T. L. (2000). Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR. Journal of Computer-Aided Molecular Design, 14(6), 593–610. https://doi.org/10.1023/a:1008121029716
Cardozo, T., Batalov, S., & Abagyan, R. (2000). Estimating local backbone structural deviation in homology models. Computers & Chemistry, 24(1), 13–31. https://doi.org/10.1016/s0097-8485(99)00044-3
Zhang, H. F., Yu, J., Chen, S., Morgan, B. P., Abagyan, R., & Tomlinson, S. (1999). Identification of the individual residues that determine human CD59 species selective activity. The Journal of Biological Chemistry, 274(16), 10969–10974. https://doi.org/10.1074/jbc.274.16.10969
Stigler, R. D., Hoffmann, B., Abagyan, R., & Schneider-Mergener, J. (1999). Soft docking an L and a D peptide to an anticholera toxin antibody using internal coordinate mechanics. Structure (London, England : 1993), 7(6), 663–670. https://doi.org/10.1016/s0969-2126(99)80087-2
Abagyan, R., & Totrov, M. (1999). Ab Initio Folding of Peptides by the Optimal-Bias Monte Carlo Minimization Procedure. Journal of Computational Physics, 151(1), 401–421. https://doi.org/10.1006/jcph.1999.6233
Derivation of the Square Root Sampling theorem for the fastest identification of the global minimum by a stochastic sampler.
Schapira, M., Totrov, M., & Abagyan, R. (1999). Prediction of the binding energy for small molecules, peptides and proteins. Journal of Molecular Recognition : JMR, 12(3), 177–190. https://doi.org/10.1002/(SICI)1099-1352(199905/06)12:3<177::AID-JMR451>3.0.CO;2-Z
Li, D., Desai-Yajnik, V., Lo, E., Schapira, M., Abagyan, R., & Samuels, H. H. (1999). NRIF3 is a novel coactivator mediating functional specificity of nuclear hormone receptors. Molecular and Cellular Biology, 19(10), 7191–7202. https://doi.org/10.1128/MCB.19.10.7191
Gates, M. A., Kim, L., Egan, E. S., Cardozo, T., Sirotkin, H. I., Dougan, S. T., Lashkari, D., Abagyan, R., Schier, A. F., & Talbot, W. S. (1999). A genetic linkage map for zebrafish: Comparative analysis and localization of genes and expressed sequences. Genome Research, 9(4), 334–347.
Zhou, Y., & Abagyan, R. (1998). How and why phosphotyrosine-containing peptides bind to the SH2 and PTB domains. Folding & Design, 3(6), 513–522. https://doi.org/10.1016/S1359-0278(98)00067-4
Srivastava, S., Osten, P., Vilim, F. S., Khatri, L., Inman, G., States, B., Daly, C., DeSouza, S., Abagyan, R., Valtschanoff, J. G., Weinberg, R. J., & Ziff, E. B. (1998). Novel anchorage of GluR2/3 to the postsynaptic density by the AMPA receptor-binding protein ABP. Neuron, 21(3), 581–591. https://doi.org/10.1016/s0896-6273(00)80568-1
Patel, I. R., Attur, M. G., Patel, R. N., Stuchin, S. A., Abagyan, R. A., Abramson, S. B., & Amin, A. R. (1998). TNF-alpha convertase enzyme from human arthritis-affected cartilage: Isolation of cDNA by differential display, expression of the active enzyme, and regulation of TNF-alpha. Journal of Immunology (Baltimore, Md. : 1950), 160(9), 4570–4579.
Maiorov, V., & Abagyan, R. (1998). Energy strain in three-dimensional protein structures. Folding & Design, 3(4), 259–269. https://doi.org/10.1016/S1359-0278(98)00037-6
Isakoff, S. J., Cardozo, T., Andreev, J., Li, Z., Ferguson, K. M., Abagyan, R., Lemmon, M. A., Aronheim, A., & Skolnik, E. Y. (1998). Identification and analysis of PH domain-containing targets of phosphatidylinositol 3-kinase using a novel in vivo assay in yeast. The EMBO Journal, 17(18), 5374–5387. https://doi.org/10.1093/emboj/17.18.5374
Yu, J., Dong, S., Rushmere, N. K., Morgan, B. P., Abagyan, R., & Tomlinson, S. (1997). Mapping the regions of the complement inhibitor CD59 responsible for its species selective activity. Biochemistry, 36(31), 9423–9428. https://doi.org/10.1021/bi970832i
Yu, J., Abagyan, R., Dong, S., Gilbert, A., Nussenzweig, V., & Tomlinson, S. (1997). Mapping the active site of CD59. The Journal of Experimental Medicine, 185(4), 745–753. https://doi.org/10.1084/jem.185.4.745
Totrov, M., & Abagyan, R. (1997). Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins, Suppl 1, 215–220. https://doi.org/10.1002/(sici)1097-0134(1997)1+<215::aid-prot29>3.3.co;2-i
Thanki, N., Zeelen, J. P., Mathieu, M., Jaenicke, R., Abagyan, R. A., Wierenga, R. K., & Schliebs, W. (1997). Protein engineering with monomeric triosephosphate isomerase (monoTIM): The modelling and structure verification of a seven-residue loop. Protein Engineering, 10(2), 159–167. https://doi.org/10.1093/protein/10.2.159
Rashin, A. A., Rashin, B. H., Rashin, A., & Abagyan, R. (1997). Evaluating the energetics of empty cavities and internal mutations in proteins. Protein Science : A Publication of the Protein Society, 6(10), 2143–2158. https://doi.org/10.1002/pro.5560061009
Mathieu, M., Modis, Y., Zeelen, J. P., Engel, C. K., Abagyan, R. A., Ahlberg, A., Rasmussen, B., Lamzin, V. S., Kunau, W. H., & Wierenga, R. K. (1997). The 1.8 A crystal structure of the dimeric peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae: Implications for substrate binding and reaction mechanism. Journal of Molecular Biology, 273(3), 714–728. https://doi.org/10.1006/jmbi.1997.1331
Maiorov, V., & Abagyan, R. (1997). A new method for modeling large-scale rearrangements of protein domains. Proteins, 27(3), 410–424. https://doi.org/10.1002/(sici)1097-0134(199703)27:3<410::aid-prot9>3.0.co;2-g
Koonin, E. V., & Abagyan, R. A. (1997). TSG101 may be the prototype of a class of dominant negative ubiquitin regulators. Nature Genetics, 16(4), 330–331. https://doi.org/10.1038/ng0897-330
Abagyan, R., Batalov, S., Cardozo, T., Totrov, M., Webber, J., & Zhou, Y. (1997). Homology modeling with internal coordinate mechanics: Deformation zone mapping and improvements of models via conformational search. Proteins, Suppl 1, 29–37. https://doi.org/10.1002/(sici)1097-0134(1997)1+<29::aid-prot5>3.3.co;2-4
Abagyan, R. A., & Totrov, M. M. (1997). Contact area difference (CAD): A robust measure to evaluate accuracy of protein models. Journal of Molecular Biology, 268(3), 678–685. https://doi.org/10.1006/jmbi.1997.0994
Abagyan, R. A., & Batalov, S. (1997). Do aligned sequences share the same fold? Journal of Molecular Biology, 273(1), 355–368. https://doi.org/10.1006/jmbi.1997.1287
Totrov, M., & Abagyan, R. (1996). The contour-buildup algorithm to calculate the analytical molecular surface. Journal of Structural Biology, 116(1), 138–143. https://doi.org/10.1006/jsbi.1996.0022
Strynadka, N. C., Eisenstein, M., Katchalski-Katzir, E., Shoichet, B. K., Kuntz, I. D., Abagyan, R., Totrov, M., Janin, J., Cherfils, J., Zimmerman, F., Olson, A., Duncan, B., Rao, M., Jackson, R., Sternberg, M., & James, M. N. (1996). Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. Nature Structural Biology, 3(3), 233–239. https://doi.org/10.1038/nsb0396-233
Goodman, A. R., Cardozo, T., Abagyan, R., Altmeyer, A., Wisniewski, H. G., & Vilcek, J. (1996). Long pentraxins: An emerging group of proteins with diverse functions. Cytokine & Growth Factor Reviews, 7(2), 191–202. https://doi.org/10.1016/1359-6101(96)00019-6
Chalikian, T. V., Totrov, M., Abagyan, R., & Breslauer, K. J. (1996). The hydration of globular proteins as derived from volume and compressibility measurements: Cross correlating thermodynamic and structural data. Journal of Molecular Biology, 260(4), 588–603. https://doi.org/10.1006/jmbi.1996.0423
Houbrechts, A., Moreau, B., Abagyan, R., Mainfroid, V., Préaux, G., Lamproye, A., Poncin, A., Goormaghtigh, E., Ruysschaert, J. M., & Martial, J. A. (1995). Second-generation octarellins: Two new de novo (beta/alpha)8 polypeptides designed for investigating the influence of beta-residue packing on the alpha/beta-barrel structure stability. Protein Engineering, 8(3), 249–259. https://doi.org/10.1093/protein/8.3.249
Cardozo, T., Totrov, M., & Abagyan, R. (1995). Homology modeling by the ICM method. Proteins, 23(3), 403–414. https://doi.org/10.1002/prot.340230314
Borchert, T. V., Kishan, K. V., Zeelen, J. P., Schliebs, W., Thanki, N., Abagyan, R., Jaenicke, R., & Wierenga, R. K. (1995). Three new crystal structures of point mutation variants of monoTIM: conformational flexibility of loop-1, loop-4 and loop-8. Structure (London, England : 1993), 3(7), 669–679. https://doi.org/10.1016/s0969-2126(01)00202-7
Totrov, M., & Abagyan, R. (1994). Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy. Nature Structural Biology, 1(4), 259–263. https://doi.org/10.1038/nsb0494-259
The first predictive global protein (cross-)docking with fully flexible interfaces, and the correct lowest energy minimum
Borchert, T. V., Abagyan, R., Jaenicke, R., & Wierenga, R. K. (1994). Design, creation, and characterization of a stable, monomeric triosephosphate isomerase. Proceedings of the National Academy of Sciences of the United States of America, 91(4), 1515–1518. https://doi.org/10.1073/pnas.91.4.1515
Argos, P., & Abagyan, R. (1994). The protein folding problem: Finding a few minimums in a near infinite space. Computers & Chemistry, 18(3), 225–231. https://doi.org/10.1016/0097-8485(94)85017-8
Abagyan, R., & Totrov, M. (1994). Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. Journal of Molecular Biology, 235(3), 983–1002. https://doi.org/10.1006/jmbi.1994.1052
Internal Coordinate Mechanics. Stochastic global optimization with continuous large moves guided by local probability distributions.
Abagyan, R., Totrov, M. & Kuznetsov, D. (1994). ICM - a new method for protein modelling and design. Applications to docking and structure prediction from the distorted native conformation. Journal of Computational Chemistry, 15488-506. https://doi.org/10.1002/jcc.540150503
Convergent global protein docking in internal coordinates
Abagyan, R., Frishman, D., & Argos, P. (1994). Recognition of distantly related proteins through energy calculations. Proteins, 19(2), 132–140. https://doi.org/10.1002/prot.340190206
Kuznetsov, D. A., & Abagyan, R. A. (1993). A technique for identifying atoms from a screen image. Journal of Molecular Graphics, 11(4), 245–247. https://doi.org/10.1016/0263-7855(93)80004-b
Gibson, T. J., Thompson, J. D., & Abagyan, R. A. (1993). Proposed structure for the DNA-binding domain of the helix-loop-helix family of eukaryotic gene regulatory proteins. Protein Engineering, 6(1), 41–50. https://doi.org/10.1093/protein/6.1.41
Eisenmenger, F., Argos, P., & Abagyan, R. (1993). A method to configure protein side-chains from the main-chain trace in homology modelling. Journal of Molecular Biology, 231(3), 849–860. https://doi.org/10.1006/jmbi.1993.1331
Borchert, T. V., Abagyan, R., Kishan, K. V., Zeelen, J. P., & Wierenga, R. K. (1993). The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: the correct modelling of an eight-residue loop. Structure (London, England : 1993), 1(3), 205–213. https://doi.org/10.1016/0969-2126(93)90021-8
Abagyan, R. A. (1993). Towards protein folding by global energy optimization. FEBS Letters, 325(1–2), 17–22. https://doi.org/10.1016/0014-5793(93)81406-p
Abagyan, R., & Argos, P. (1992). Optimal protocol and trajectory visualization for conformational searches of peptides and proteins. Journal of Molecular Biology, 225(2), 519–532. https://doi.org/10.1016/0022-2836(92)90936-e
Gromova, I. I., Buchman, V. L., Abagyan, R. A., Ulyanov, A. V., & Bronstein, I. B. (1990). Sequence dependent modulating effect of camptothecin on the DNA-cleaving activity of the calf thymus type I topoisomerase. Nucleic Acids Research, 18(3), 637–645. https://doi.org/10.1093/nar/18.3.637
Eisenhaber, F., Tumanyan, V. G., & Abagyan, R. A. (1990). Structure of the hydration shells of oligo(dA-dT).oligo(dA-dT) and oligo(dA).oligo(dT) tracts in B-type conformation on the basis of Monte Carlo calculations. Biopolymers, 30(5–6), 563–581. https://doi.org/10.1002/bip.360300509
Abagyan, R. A., Mironov, V. N., Chernov, B. K., Chuprina, V. P., & Ulyanov, A. V. (1990). Electrophoretic behavior of d(GGAAAAAAGG)n, d(CCAAAAAACC)n, and (CCAAAAAAGG)n and implications for a DNA bending model. Nucleic Acids Research, 18(4), 989–992. https://doi.org/10.1093/nar/18.4.989
Mazur, A. K., & Abagyan, R. A. (1989). New methodology for computer-aided modelling of biomolecular structure and dynamics. 1. Non-cyclic structures. Journal of Biomolecular Structure & Dynamics, 6(4), 815–832. https://doi.org/10.1080/07391102.1989.10507739
Abagyan, R. A., & Mazur, A. K. (1989). New methodology for computer-aided modelling of biomolecular structure and dynamics. 2. Local deformations and cycles. Journal of Biomolecular Structure & Dynamics, 6(4), 833–845. https://doi.org/10.1080/07391102.1989.10507740
Abagyan, R. A., & Maiorov, V. N. (1989). An automatic search for similar spatial arrangements of alpha-helices and beta-strands in globular proteins. Journal of Biomolecular Structure & Dynamics, 6(6), 1045–1060. https://doi.org/10.1080/07391102.1989.10506535
Chuprina, V. P., & Abagyan, R. A. (1988). Structural basis of stable bending in DNA containing An tracts. Different types of bending. Journal of Biomolecular Structure & Dynamics, 6(1), 121–138. https://doi.org/10.1080/07391102.1988.10506486
Chuprina, V. P., & Abagyan, R. A. (1988). Anomalous properties of adenine.thymine tracts. Nature, 332(6160), 117. https://doi.org/10.1038/332117a0
Abagyan, R. A., & Maiorov, V. N. (1988). A simple qualitative representation of polypeptide chain folds: Comparison of protein tertiary structures. Journal of Biomolecular Structure & Dynamics, 5(6), 1267–1279. https://doi.org/10.1080/07391102.1988.10506469
Ivanitskiĭ, G. R., Esipova, N. G., Abagyan, R. A., & Shnol’, S. E. (1985). [Block improvement of the genetic text as a factor of acceleration of biological evolution]. Biofizika, 30(3), 418–421.
Abagyan, R. A., Tumanian, V. G., & Esipova, N. G. (1984). [Two types of tripeptide conformation in collagen. Calculation of the structure of (Gly-Pro-Ser)n and (Gly-Val-Hyp)n polytripeptides]. Bioorganicheskaia khimiia, 10(4), 476–482.
Abagyan, R. A. (1983). [Diffraction from the alternating helix]. Biofizika, 28(3), 388–392.
Abagyan, R. A. (1983). [Arrangement of molecular packing of collagen in fibrils]. Biofizika, 28(3), 498–500.
Rogulenkova, V. N., Abagyan, R. A., Tumanian, V. G., & Esipova, N. G. (1981). [Diffraction effects on x-rays of the oligotripeptide (Gly-Pro-Pro)10, isomorphic to collagen]. Biofizika, 26(4), 734–736.