Professor, Departments of Biopharmaceutical Sciences and Laboratory Medicine, UCSF
Additional Websites
Education
University of Minnesota, St. Paul, MN, BS, 1986, Biochemistry
University of Minnesota, Minneapolis, MN, BS, 1986, Computer Science
Carnegie Mellon University, Pittsburgh, PA, MS, 1989, Computer Science
Carnegie Mellon University, Pittsburgh, PA, PhD, 1991, Computer Science
Professional Experience
-
1983-1986
Research Engineer, Machine Vision Technology, Honeywell, Minneapolis, MN
-
1992
Principal Research Scientist, Multi-Sensor Signal Processing. Alliant Techsystems (formerly Honeywell), Minneapolis, MN
-
1992-1996
Senior Scientist and Group Leader of Computational Sciences, Arris Pharmaceutical, So. San Francisco, CA
-
1996-1997
Principal Scientist and Group Leader of Computational Sciences, MetaXen LLC, Hayward, CA
-
1997-present
Founder and Chief Scientist, BioPharmics, San Mateo, CA
-
1998-1999
Director of Applied Computing, Iconix Pharmaceuticals, Mountain View, CA
-
1999-present
Full Member, UCSF Cancer Center, University of California, San Francisco, CA
-
1999-2002
Director of Informatics, UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
-
1999-2002
Associate Adjunct Professor, Cancer Research Institute and Department of Laboratory Medicine, University of California, San Francisco, CA
-
2002-present
Director, Informatics Core, UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
-
2002-2007
Associate Professor, Cancer Research Institute and Department of Laboratory Medicine, University of California, San Francisco, CA
-
2004-2007
Associate Professor, Department of Biopharmaceutical Sciences, University of California, San Francisco, CA
-
2007-present
Professor, Cancer Research Institute, Department of Biopharmaceutical Sciences, and Department of Laboratory Medicine, University of California, San Francisco, CA
Selected Publications
- Varela R, Walters WP, Goldman BB, Jain AN. Iterative refinement of a binding pocket model: active computational steering of lead optimization. J Med Chem. 2012 Oct 25; 55(20):8926-42.
View on PubMed - Spitzer R, Jain AN. Surflex-Dock: Docking benchmarks and real-world application. J Comput Aided Mol Des. 2012 Jun; 26(6):687-99.
View on PubMed - Jones DA, Weerackody R, Rathod K, Behar J, Gallagher S, Knight CJ, Kapur A, Jain AK, Rothman MT, Thompson CA, Mathur A, Wragg A, Smith EJ. Successful recanalization of chronic total occlusions is associated with improved long-term survival. JACC Cardiovasc Interv. 2012 Apr; 5(4):380-8.
View on PubMed - Jain AN, Cleves AE. Does your model weigh the same as a duck? J Comput Aided Mol Des. 2012 Jan; 26(1):57-67.
View on PubMed - Jones DA, Jain AK. Percutaneous balloon pericardiotomy for recurrent malignant pericardial effusion. J Thorac Oncol. 2011 Dec; 6(12):2138-9.
View on PubMed - Yera ER, Cleves AE, Jain AN. Chemical structural novelty: on-targets and off-targets. J Med Chem. 2011 Oct 13; 54(19):6771-85.
View on PubMed - Spitzer R, Cleves AE, Jain AN. Surface-based protein binding pocket similarity. Proteins. 2011 Sep; 79(9):2746-63.
View on PubMed - Jain AN. QMOD: physically meaningful QSAR. J Comput Aided Mol Des. 2010 Oct; 24(10):865-78.
View on PubMed - Nicholls A, McGaughey GB, Sheridan RP, Good AC, Warren G, Mathieu M, Muchmore SW, Brown SP, Grant JA, Haigh JA, Nevins N, Jain AN, Kelley B. Molecular shape and medicinal chemistry: a perspective. J Med Chem. 2010 May 27; 53(10):3862-86.
View on PubMed - Langham JJ, Cleves AE, Spitzer R, Kirshner D, Jain AN. Physical binding pocket induction for affinity prediction. J Med Chem. 2009 Oct 8; 52(19):6107-25.
View on PubMed - Jain AN. Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation. J Comput Aided Mol Des. 2009 Jun; 23(6):355-74.
View on PubMed - Langham JJ, Jain AN. Accurate and interpretable computational modeling of chemical mutagenicity. J Chem Inf Model. 2008 Sep; 48(9):1833-9.
View on PubMed - Jain AN, Nicholls A. Recommendations for evaluation of computational methods. J Comput Aided Mol Des. 2008 Mar-Apr; 22(3-4):133-9.
View on PubMed - Pham TA, Jain AN. Customizing scoring functions for docking. J Comput Aided Mol Des. 2008 May; 22(5):269-86.
View on PubMed - Jain AN. Bias, reporting, and sharing: computational evaluations of docking methods. J Comput Aided Mol Des. 2008 Mar-Apr; 22(3-4):201-12.
View on PubMed - Cleves AE, Jain AN. Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery. J Comput Aided Mol Des. 2008 Mar-Apr; 22(3-4):147-59.
View on PubMed - Jain AN. Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. J Comput Aided Mol Des. 2007 May; 21(5):281-306.
View on PubMed - Kingsley CB, Kuo WL, Polikoff D, Berchuck A, Gray JW, Jain AN. Magellan: a web based system for the integrated analysis of heterogeneous biological data and annotations; application to DNA copy number and expression data in ovarian cancer. Cancer Inform. 2006; 2:10-21.
View on PubMed - Chin K, DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, Kuo WL, Lapuk A, Neve RM, Qian Z, Ryder T, Chen F, Feiler H, Tokuyasu T, Kingsley C, Dairkee S, Meng Z, Chew K, Pinkel D, Jain A, Ljung BM, Esserman L, Albertson DG, Waldman FM, Gray JW. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell. 2006 Dec; 10(6):529-41.
View on PubMed - Pham TA, Jain AN. Parameter estimation for scoring protein-ligand interactions using negative training data. J Med Chem. 2006 Oct 5; 49(20):5856-68.
View on PubMed
View on UCSF Profiles
