Ajay N. Jain, PhD

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
jain_ajay

Professor, Departments of Biopharmaceutical Sciences and Laboratory Medicine, UCSF

ajain@jainlab.org

Phone: (415) 502-7242 (voice)
Box 0128, UCSF
San Francisco, CA 94143-0128

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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

Honors & Awards

  • 2010
    Levinthal Lecturer, Eleventh International CUP Symposium in Molecular Modeling

Selected Publications

  1. Yera ER, Cleves AE, Jain AN. Prediction of off-target drug effects through data fusion. Pac Symp Biocomput. 2014; 19:160-71.
    View on PubMed
  2. Spitzer R, Cleves AE, Varela R, Jain AN. Protein function annotation by local binding site surface similarity. Proteins. 2014 Apr; 82(4):679-94.
    View on PubMed
  3. Varela R, Cleves AE, Spitzer R, Jain AN. A structure-guided approach for protein pocket modeling and affinity prediction. J Comput Aided Mol Des. 2013 Nov; 27(11):917-34.
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  4. Jain A, Poonia B, So EC, Vyzasatya R, Burch EE, Olsen HS, Mérigeon EY, Block DS, Zhang X, Schulze DH, Hanna NN, Twadell WS, Yfantis HG, Chan SL, Cai L, Strome SE. Tumour antigen targeted monoclonal antibodies incorporating a novel multimerisation domain significantly enhance antibody dependent cellular cytotoxicity against colon cancer. Eur J Cancer. 2013 Oct; 49(15):3344-52.
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  5. 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.
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  6. Spitzer R, Jain AN. Surflex-Dock: Docking benchmarks and real-world application. J Comput Aided Mol Des. 2012 Jun; 26(6):687-99.
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  7. 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.
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  8. Jain AN, Cleves AE. Does your model weigh the same as a duck? J Comput Aided Mol Des. 2012 Jan; 26(1):57-67.
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  9. Jones DA, Jain AK. Percutaneous balloon pericardiotomy for recurrent malignant pericardial effusion. J Thorac Oncol. 2011 Dec; 6(12):2138-9.
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  10. Yera ER, Cleves AE, Jain AN. Chemical structural novelty: on-targets and off-targets. J Med Chem. 2011 Oct 13; 54(19):6771-85.
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  11. Spitzer R, Cleves AE, Jain AN. Surface-based protein binding pocket similarity. Proteins. 2011 Sep; 79(9):2746-63.
    View on PubMed
  12. Jain AN. QMOD: physically meaningful QSAR. J Comput Aided Mol Des. 2010 Oct; 24(10):865-78.
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  13. 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.
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  14. 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.
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  15. 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.
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  16. Langham JJ, Jain AN. Accurate and interpretable computational modeling of chemical mutagenicity. J Chem Inf Model. 2008 Sep; 48(9):1833-9.
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  17. Jain AN, Nicholls A. Recommendations for evaluation of computational methods. J Comput Aided Mol Des. 2008 Mar-Apr; 22(3-4):133-9.
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  18. Pham TA, Jain AN. Customizing scoring functions for docking. J Comput Aided Mol Des. 2008 May; 22(5):269-86.
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  19. Jain AN. Bias, reporting, and sharing: computational evaluations of docking methods. J Comput Aided Mol Des. 2008 Mar-Apr; 22(3-4):201-12.
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  20. 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

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