Website Of The Abagyan Lab
We dock compounds, proteins and peptides, do protein modeling, structure based lead discovery, drug repurposing, cheminformatics, molecular design, structural modeling and drug binding for GPCRs, kinases, nuclear receptors, green chemistry, structural basis of adverse effects.
News, Aug-11-2011: The GPCR Dock 2010 modeling and docking contest article has been published and got the journal cover. More info and website
Study of retroviral capsid shapes, stability and assembly using macromolecular docking of flexible oligomeric protein subunits and simplified coarse-grain models. View the project
Variation a small molecule binding pocket in terms of composition, protonation and tautomerization, and conformation depending on a bound ligand. View the project
Lab computing infrastructure. View the project
Welcome!
In 2009 we crossed the N.Torrey Pines road and moved from TSRI to the University of California, San Diego. Our new home is the Skaggs School of Pharmacy and Pharmaceutical Sciences and the San Diego Supercomputer Center. This lab research is focused on the following topics:- Discovering small molecule inhibitors of protein function, protein-protein interaction, including allosteric inhibitors in collaboration with experimental laboratories. Check our Research page for ten recent de novo structure based discovery projects.
- Developing algorithms, benchmarks and parameters for induced fit docking, ligand screening and profiling
- Kinase exosites and non-traditional inhibitors. Developing and applying methods for de novo identification of specific kinase inhibitors (see our recent DOLPHIN method).
- Building detailed atomic models of membrane proteins. GPCRs. Modeling by homology. Ligand-guided modeling. Understanding the structural basis of agonist-GPCR interactions.
- Nuclear Receptors (NR): building a comprehensive structural panel for understanding ligand-NR binding geometry, ligand screening and ligand specificity profiling, ligand guided building of antagonist bound models for AR.
- Target based drug repurposing. Discovering secondary activities of marketed drugs
- Structural Bioinformatics, predicting effects of mutations and SNPs, pharmacogenomics, predicting protein patches involved in protein, peptide, membrane or small molecule interactions.
- Protein docking. Docking proteins and peptides to other proteins. Docking and refining with low resolution electron density and various experimental restraints. Predicting re-structuring of flexible protein parts upon formation of a transient ternary complex.
- Internal coordinate mechanics and force fields.
- Cheminformatics, QSAR and ADMET predictions.
Lab Servers
- The pocketome database (NEW) [Pocketome]
- GPCR Modeling and Docking contest (CXCR4 with a small molecule, peptide, D3) [GPCRdock2010]
- Predict likely protein-protein interaction patches [PIER]
- Generate Elastic Network Normal Mode guided multiple receptor conformations [MRC]
- Compute Similar Contacts between two protein-ligand complexes [SimiCon]
We collaborate with biologists, structural biologists, medicinal chemists, and pharmacologists. If you can test activity of a compound you are a potential collaborator. In particular, if your protein is a molecular target in treatment of a cancer or a neglected disease.