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RESEARCH POSITIONS

• Associate Professional Research Scientist, University of California, San Francisco (2007-present)
• Assistant Professional Research Scientist, University of California, San Francisco (2003-2007)
• Research Associate, The Rockefeller University, New York (2000-2003)

EDUCATION

• Ph.D. Molecular Biophysics, Indian Institute of Science, Bangalore, India (1995-2000)
• M.Sc. Physics, University of Hyderabad, Hyderabad, India (1993-1995)

RESEARCH EXPERIENCE

• Large-Scale Protein Structure Modeling

  Mentor: Prof. Andrej Sali (Rockefeller University, NY; University of California, San Francisco, CA)
  • Leading the development of Modpipe, a modular large-scale protein structure modeling software pipeline.
  • Developed methods and strategies to improve computational efficiency and accuracy of the pipeline.
  • Created and maintain Modweb, a widely used web-interface for Modpipe.
  • Modpipe used to calculate models for over 3 million protein sequences, publicly available through Modbase, the largest comprehensive database of protein structure models.
  • Applications of Modpipe include prediction of protein-protein and host-pathogen interactions, analysis of SNPs, genome annotation and small-molecule docking.

• Structural Characterization of Macromolecular Assemblies

  Collaborators: Profs. Guenter Blobel (Rockefeller University, NY), Joachim Frank (Wadsworth Center, Albany, NY), Christopher Akey (Boston University, MA)
  • Used Modpipe to create an exhaustive inventory of protein structure models for docking into and subsequent interpretation of low-resolution cryo- electron density maps of ribosomes from S. cerevisiae, E. coli, C. lupus and T. lanuginosus.
  • Identified and spatially characterized proteins involved in ribosomal function and dynamics.

• Protein Structure Modeling for Virtual Screening

  Collaborator: Prof. Brian K. Shoichet (Univ. of California, San Francisco, CA)
  • Developed and implemented a protocol in Modpipe to enhance the geometrical accuracy of binding sites in protein structure models to facilitate ligand-docking and virtual screening.
  • Predicted substrate specificities for members of the mechanistically diverse amidohydrolase superfamily by in silico docking.

• Target-Selection and Validation for Structural Genomics

  Collaborators: Stephen K. Burley, New York Structural Genomics Research Consortium (SGX Pharmaceuticals, Inc., CA)
  • Applied Modpipe to select targets for structure determination towards maximizing structural coverage of protein families.
  • Modweb routinely used to validate modeling impact of newly determined structures.

• Conformational Analysis of Protein Structures

  Supervisor: Prof. C. Ramakrishnan (Indian Institute of Science, Bangalore, India)
  • Identified deterministic features and derived conformational rules governing the adoption of non-repetitive structures in proteins.
  • Proposed and tested a hypothesis to explain the effect of solvent molecules on the stereochemical code of glycyl residues.
  • Characterized the structural role of isolated extended beta-strands in proteins.

SOFTWARE

• Modpipe, a software pipeline for large-scale protein structure modeling (Licensed to Accelrys Inc. & SGX Pharmaceuticals Inc. 2000-2004).
• Modeller, a program for comparative protein structure modeling by satisfaction of spatial restraints (Licensed to Accelrys Inc. since 1994).
• Modbase, a comprehensive database for protein structure models (Licensed to Structural Genomix Inc. 2000-2004).
• Modweb, a web-server for protein structure modeling.

CONSULTING & INDUSTRY

• Accelrys Inc. (2003-present) Comparative protein structure modeling.
• Intel Corporation (2003) Optimization of algorithms for IPF architecture.
• SGX Pharmaceuticals Inc. (2002-2003) Large-scale protein structure modeling.

INVITED PRESENTATIONS

• Eighteenth Annual World Molecular Engineering Network Conference, San Jose del Cabo, Mexico. Apr 29-May 3, 2007 (speaker).
• Workshop on Target Selection for the Protein Structure Initiative, NIH/NIGMS, Bethesda, MD, USA. Jun. 26-27, 2006 (speaker).
• Symposium on Digital Biology: An Emerging Paradigm, NIH/BISTI, Bethesda, MD, USA. Nov. 6-7, 2003 (speaker).
• Workshop on High-accuracy Comparative Modeling Workshop, NIH/NIGMS, Bethesda, MD, USA. Oct. 20-21, 2003 (observer).

SELECTED PUBLICATIONS (Total: 35; Click here for complete list)

1. Structure of the mammalian 80S ribosome at 8.7Å resolution.

   Chandramouli P, Topf M*, Ménéret JF*, Eswar N*, Gutell RR, Sali A and Akey CW.
   (Submitted)
   (*These authors contributed equally to this work).
   

2. Comparative modeling of drug target proteins.

   Eswar N and Sali A
   In Comprehensive Medicinal Chemistry II. 2007. (Eds: Taylor JB, Triggle DJ). pp 215-236.
   Elsevier Ltd, Oxford, UK.

3. MODBASE: a database of annotated comparative protein structure models and associated resources.

   Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, Shen MY, Kelly L, Melo F, Sali A.
   Nucleic Acids Res. 2006. 34:D291-295.
   

4. Structure determination of macromolecular complexes by experiment and computation.

   Alber F*, Eswar N* and Sali A.
   In Practical Bioinformatics. 2004. (Ed: Bujnicki JM). pp 73-96.
   Springer-Verlag, Germany.
   (*These authors contributed equally to this work).

5. Stranded in isolation: structural role of isolated extended strands in proteins.

   Eswar N, Ramakrishnan C, Srinivasan N.
   Protein Eng. 2003. 16:331-339.
   

6. Tools for comparative protein structure modeling and analysis.

   Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A.
   Nucleic Acids Res. 2003. 31:3375-3380.
   

7. Influence of solvent molecules on the stereochemical code of glycyl residues in proteins.

   Eswar N, Nagarajaram HA, Ramakrishnan C, Srinivasan N.
   Proteins. 2002. 49:326-334.
   

8. Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions.

   Spahn CM, Beckmann R, Eswar N, Penczek PA, Sali A, Blobel G, Frank J.
   Cell. 2001. 107:373-386.
   

9. Architecture of the protein-conducting channel associated with the translating 80S ribosome.

   Beckmann R, Spahn CM, Eswar N, Helmers J, Penczek PA, Sali A, Frank J, Blobel G.
   Cell. 2001. 107:361-372.
   

10. Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis.

    Bonanno JB, Edo C, Eswar N, Pieper U, Romanowski MJ, Ilyin V, Gerchman SE, Kycia H, Studier FW, Sali A, Burley SK.
    Proc Natl Acad Sci USA. 2001. 98:12896-12901.
    

11. Protein structure modeling for structural genomics.

    Sanchez R, Pieper U, Melo F, Eswar N, Marti-Renom MA, Madhusudhan MS, Mirkovic N, Sali A.
    Nat Struct Biol. 2000.7:986-990.
    

12. Secondary structures without backbone: an analysis of backbone mimicry by polar side chains in protein structures.

    Eswar N, Ramakrishnan C.
    Protein Eng. 1999. 12:447-455.
    

PROFESSIONAL ACTIVITIES

• Peer Review: Reviewed manuscripts for Bioinformatics, BMC-Bioinformatics, BMC-Evolutionary Biology, Chemistry & Biology, ChemMedChem, FEBS Letters, Gene, In Silico Biology, Journal of Computer-aided Molecular Design, Journal of Molecular Graphics & Modeling, Journal of Molecular Modeling, Proteins, Protein Science, Protein Engineering Design & Selection, Structure.
• Mentorship: Michael Mysinger (rotation student; derivation of rules for modeling protein side-chains), Kenneth S. Krauter (visiting scientist; modeling of oligomeric proteins), Nima Fayazmanesh (rotation student; modeling of Hsp90).

HONORS & ACHIEVEMENTS

• Senior Research Fellowship, Indian Institute of Science, Bangalore, India (1997-2000)
• Junior Research Fellowship, Indian Institute of Science, Bangalore, India (1995-1997)
• Summer Research Scholarship, Center for Cellular and Molecular Biology, Hyderabad, India (1994)
• Ranked in the top 1% at the National Standard Examination in Physics, Indian Association of Physics Teachers, Chennai, India (1992)
• Gold Medal for academic proficiency, Loyola College, Chennai, India (1991)