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
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
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
San Diego Supercomputer Center
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
Cheminformatics, QSAR and ADMET
- 2013 GPCR Modeling and Docking contest (5HT1B and 2B with ergotamine, SMO with two small molecules) (NEW) [GPCRdock2013]
- The pocketome database [Pocketome]
- 2010 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
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.
Last updated: 2014/05/13