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Research and Clinical Interests

Predictive computational modeling encompasses all of the work in the Jain Lab. This takes primary form in algorithmic approaches for drug discovery. The primary areas of research in the lab are: 1) methods for docking small molecules to proteins using empirically derived scoring functions, 2) methods for inducing the shape of a protein binding pocket given the structures and affinities of ligands that bind the pocket competitively, 3) generalized surface-based approaches to computing molecular similarity, both among small molecules and proteins, 4) approaches for modeling and prediction of polypharmacology based on molecular structure, and 5) applications of such methods for cancer drug discovery. All of the approaches share their roots in the use of sophisticated computational algorithms involving object representation, function optimization, and search.

Selected Publications

• Langham, J.J., Cleves, A.E., Spitzer, R., Kirshner, D., and Jain, A.N. (2009). Physical Binding Pocket Induction for Affinity Prediction. J Med Chem, 52, 6107-6125.
• Jain, A.N. (2009). Effects of Protein Conformation in Docking: Improved Pose Prediction Through Protein Pocket Adaptation. J Computer-Aided Molecular Design, 23, 355-374.
• Pham, T. A. and Jain, A.N. (2008). Customizing Scoring Functions for Docking. J Computer-Aided Molecular Design, 22, 269-286.
• Langham, J.J. and Jain, A.N. (2008). Accurate and Interpretable Computational Modeling of Chemical Mutagenicity. J Chem Inf Model, 48, 1833-1839.
• Jain, A.N. (2007). Surflex-Dock 2.1: Robust Performance from Ligand Energetic Modeling, Ring Flexibility, and Knowledge-Based Search. J Computer-Aided Molecular Design, 21, 281-306.
• Cleves, A. E. and Jain, A.N. (2006). Robust Ligand-Based Modeling of the Biological Targets of Known Drugs. J Med Chem, 49, 2921-2938
• Pham, T. A. and Jain, A.N. (2006). Parameter Estimation for Scoring Protein-Ligand Interactions using Negative Training Data. J Med Chem, 49, 5856-5868.

• Professor
• Laboratory Medicine
• Bioengineering and Therapeutic Sciences

Specialty Area

• Computational Biology
• Biophysics
• Chemistry

Contact Information

• ajain@jainlab.org
• Phone: 415-502-7242
• Fax: 650-240-1781

• Box 0128

Web Site

• http://www.jainlab.org

Other UCSF Organizational Association(s)

Member

• UCSF Helen Diller Family Comprehensive Cancer Center