Shankar Subramaniam

 Contact Info:

Shankar Subramaniam
Department of Bioengineering
Department of Chemistry & Biochemistry
San Diego Supercomputing Center
University of California at San Diego
9500 Gilman Drive
La Jolla, CA 92037
shankar@sdsc.edu

RESEARCH PROFILE

Shankar Subramaniam is currently a Professor of Bioengineering and Chemistry and Biochemistry at the University of California at San Diego. He also has a joint appointment at the San Diego Supercomputing Center. Before he moved to UCSD (fall ’99), he was the Director of the computational biology group at the National Center for Supercomputing Applications (NCSA) and a Professor of Biochemistry, Molecular and Integrative Physiology, Chemical Engineering and Electrical & Computer Engineering at the University. His present research focuses several important aspects of computational biology. These include web-based approaches to bioinformatics, going from protein sequence to structure and function and studying protein recognition and function.

AFFILIATIONS:

Professor:
  • Department of Bioengineering
  • Department of Chemistry & Biochemistry
  • San Diego Supercomputing Center

EDUCATION:

  • B.Sc., (Chemistry) Osmania University 1972 (Recipient of gold medal for ranking first in the University)
  • M.Sc., (Physical Organic Chemistry) Osmania University 1974 (First Class with distinction)
  • Ph.D., (Chemistry) Indian Institute of Technology Kanpur 1982

HONORS:

  • The College of Engineering, University of Illinois Advisor’s List, 1997.
  • Smithsonian Foundation Citation for Innovation in Computing, 1997.
  • Council of Scientific and Industrial Research Fellowship 1974-1976.
  • Indian National Merit Scholarship 1972-1974.
  • Thatte memorial gold medal for ranking first in Bachelor's degree 1972.

Recent Publications

  • Rojnuckarin and Subramaniam, Knowledge-Based Potentials for Protein Structure, Proteins - Structure, Function and Genetics, 36: 54-67, 1999.
  • D. Livesay and S. Subramaniam. pH dependence of antibody-hapten association. Molecular Immunology 36: 397-410, 1999.
  • C. Gibas, P. Jambeck and S. Subramaniam. Role of pH in antibody-antigen complexation, Methods, Academic Press, Ed. (Linthicum & Subramaniam) 1999 (in print).
  • M. Viswanathan and S. Subramaniam. Molecular Dynamics Simulations of Antibody-Hapten Complexes, Methods, Academic Press, Ed. (Linthicum & Subramaniam) 1999 (in print).
  • G. Altobelli & S. Subramaniam. Kinetics of Association of Anti-lysozyme Monoclonal Antibody D44.1 and Hen-egg Lysozyme. Biophys. J. (in print).
  • S. W. Chiu, S. Subramaniam and E. Jakobsson, Simulation Study of Gramicidin/Lipid Bilayer System in excess water and lipid I. Structure of the Molecular Complex, Biophysical Journal, 76:1929-38, 1999.
  • S. W. Chiu, S. Subramaniam and E. Jakobsson, Simulation Study of Gramicidin/Lipid Bilayer System in excess water and lipid II. Rates and Mechanisms of Water Transport, Biophysical Journal, 76:1939-50, 1999.
  • M. Clark, H.L. Scott, E. Jakobsson & S. Subramaniam, Simulation parameters for liquid hydrocarbons, J. Comput. Chem. 1999 (in print) 1999.
  • S. Subramaniam. The Biology Workbench: A Seamless Database and Analysis Environment for the Biologist, in BioinformaticsÓ, Proteins 32: 1-2, 1998.
  • A. Rojnuckarin, S. Kim, S. Subrmaniam. Brownian Dynamics Simulations of Protein Folding: Access to Milliseconds Time Scale and Beyond. Proc. Natl. Acad. Sci. USA. 95:4288-4292, 1998.
  • S. Sivasankar, S. Subramaniam and D. Leckband. Direct Measurement of the pH-Dependent Electrostatic Properties of a Protein Surface. Proc. Natl. Acad. Sci. USA 95: 12961-12966.1998.
  • J. Xiong, S. Subramaniam and Govindjee. A knowledge-based three dimensional model of the Photosystem II reaction center of Chlamydomonas reinhardtii. Photosynthesis Research 56: 229-254, 1998.
  • Jie Liang, Pamidinghantam Sudhakar, Herbert Edelsbrunner, Ping Fu and Shankar Subramaniam. Analytical Shape Computing in Macromolecules. I. Calculation of Surface Areas and Volumes in Proteins. Proteins 33:1-17 1998.
  • Jie Liang, Pamidinghantam Sudhakar, Herbert Edelsbrunner, Ping Fu and Shankar Subramaniam. Analytical Shape Computing in Macromolecules. II. Inaccessible Voids and Interfacial Regions in Proteins. Proteins 33:18-29 1998.
  • H.L. Scott, E. Jakobsson, S. Subramaniam. Simulations of Lipid Membranes with Atomic Resolution. Comput. Phys. 12: 328-333, 1998.
  • C. Gibas, S. Subramaniam, J.A. McCammon, B. Braden, R.J. Poljak. Electrostatic and Structural Factors in Antibody-Antigen Interactions. Biochemistry 36(50): 15599-15614, 1997.
  • J. Liang and S. Subramaniam. Computing Molecular Electrostatics A Boundary- Element Method for Protein Electrostatics. Biophys. J. 73: 1830-1841, 1997.
  • C. Gibas and S. Subramaniam. Rules for Design of a Soluble Bacteriorhodopsin. Prot. Eng. 10: 1175-1190, 1997.
  • G. Pappas and S. Subramaniam. An Evaluation of Protein Secondary Structure Prediction Algorithms. Tech. In Prot. Chem. VIII: 783-794, 1997.
  • J. Xiong, S. Subramaniam and Govindjee. Modeling of D1/D2 proteins of the photosystem II reaction center of the cyanobacterium synechocystis sp. PCC 6803 and its implications to herbicide and bicarbonate binding. Prot. Sci. 5: 2054-2073, 1996.
  • C. Singh, R. Sankararamakrishnan, S. Subramaniam, and E. Jakobsson. Solvation and Water Permeation of a Putative Model for the Pore Region of the Voltage-Gated Sodium Channel Biophys. J. 71:2276-2288, 1996.
  • M. Viswanathan, D.W. Pledger, S.Y. Tetin, D.S. Linthicum and S. Subramaniam. Modeling the Structure of the Combining Site of an Antisweet Taste Ligand Monoclonal Antibody NC 10.14. Biopolymers 39: 395-406, 1996.
  • S. Subramaniam, D.K. Tcheng and J.M. Fenton. Knowledge-Based Methods for Protein Structure Refinement and Prediction. In Proceedings of the Fourth International Conference on Intelligent Systems in Molecular Biology, St. Louis, 1996, Ed. David States et al., AAAI Press, California. pp. 218-229, 1996.
  • C. Gibas and S. Subramaniam. Explicit Solvent Models in Protein pKa Calculations. Bioph. J 71: 138-147,1996.
  • C. Mandal, M. M. Anchin, S. Subramaniam and D. S. Linthicum. ABGEN: A knowledge-Based Authomated Approach for Antibody Structure Modeling Nature - BioTechnology 14(3): 323-328,1996.
  • L.Tang, T. G. Ebrey, and S.Subramaniam. Modeling the Structure of Visual Pigments. Isr. J. Chem. 35, 198-209, 1995.
  • T. Ioerger, L. Rendell and S. Subramaniam. Change of representation to improve protein fold-class prediction. Machine Learning Journal 21:151-176, 1995.
  • R. E. Kozack, M.J. D'Mello and S. Subramaniam. Computer Modeling of Electrostatic Steering and Orientational Effects in Antibody-Antigen Association. Biophys. J. 68(3): 807-814, 1995.
  • S. W. Chiu, M. Clark, V. Balaji, S. Subramaniam, H.L. Scott and E. Jakobsson. Incorporation of Surface Tension into Molecular Dynamics Simulation of an Interface: A Fluid Phase Lipid Bilayer Membrane. Biophys. J. 69(4):1230-1245, 1995.
  • M. Viswanathan, J. M. Anchin, P. R. Droupadi, C. Mandal, D.S. Linthicum, and S. Subramaniam. Structural Predictions of the Binding Site Architecture for Monoclonial Antibody NC6.8 using Ligand Binding, Spectroscopy and Computer-Aided Molecular Modeling Bioph. J. 69(3): 741-753, 1995.
  • Jakobsson, E., Subramaniam, S., and H. L. Scott. In: Strategic issues in molecular dynamics simulations of membranes in: Membrane Structure and Dynamics, K. Merz and B. Roux, eds. Birkhauser, Boston, 1995.
  • M. Holst, R.E. Kozack, F.Saied, and S. Subramaniam. Treatment of Electrostatic Effects in Proteins: Multigrid-Based- Newton Iterative Method for Solution of the Full Nonlinear Poisson-Boltzmann Equation. Proteins: Structure, Function and Genetics. 18(3): 231-245, 1994.
  • S.Subramaniam. Protein Structure Prediction-Past and Present. In: Protein Structure by Distance Analysis, Ed. H. Bohr & S. Brunak, IOS Press, 1994, pp 3-14.
  • M. Holst, R. E. Kozack, F. Saied, S. Subramaniam. Protein Electrostatics: Rapid Multigrid-Based Newton Algorithm for Solution of the Full Nonlinear Poisson-Boltzmann Equation. J. Biomol. Struct. Dyn. 11(6): 1437-1445, 1994.
  • K. E. Forsten, R. E. Kozack, D. A. Lauffenberger, and S. Subramaniam. Numerical Solution of the Nonlinear Poisson-Boltzmann Equation for a Membrane-Electrolyte System. J. Phys. Chem. 98: 5580-5586, 1994.
  • S. P. Slagle, R. E. Kozack and S. Subramaniam. Role of Electrostatics in Antibody-antigen Association: Anti-hen Egg Lysozyme/Lysozyme Complex (HyHEL-5/HEL) J. Biomol. Struct. Dyn. 12: 439-456, 1994.
  • R. Susnow, C. Schutt ,H. Rabitz and S. Subramaniam. Conformational Analysis of Dipeptides - A Sensitivity Analysis Approach. J. Comp. Chem. 15(9): 947-962, 1994.
  • J. M. Anchin, C. Mandal, C. Culberson, S. Subramaniam and D. S. Linthicum. Computer-aided Modeling of the Binding Site Architecture for Eight Monclonal Antibodies that Bind a High Potency Guanidinium Sweetener. J. Mol. Graphics 12: 257-266, 1994.
  • M. Reczko, H. Bohr, S.Subramaniam, S. Pamidinghantam and A. Hatzigeorgiou. Fold-Class Prediction by Neural Network. In: Protein Structure Prediction-Past and Present. In: Protein Structure by Distance Analysis, Ed. H. Bohr & S. Brunak, IOS Press, 1994, pp 277-286.
  • R.E. Kozack and S. Subramaniam. Brownian Dynamics Simulations of Molecular Recognition in an Antibody-antigen System. Protein Science 2: 915-926, 1993.
  • K. R. Rodgers, C. Su, S. Subramaniam and T. G. Spiro. Hemoglobin T-R Quaternary Structure and Dynamics from Simultaneous Monitoring of Tyrosine and Tryptophan UV Resonance Raman Signals. J. Am. Chem. Soc. 114: 3697-3709, 1992.
  • D. Bassolino, R. E. Bruccoleri & S. Subramaniam. Modeling the Antigen Combining Site of an Anti-dinitrophenyl Antibody. Protein Science 1: 1465-1476, 1992.
  • L. J. Nell, J. A. McCammon and S. Subramaniam. Anti-insulin Antibody. Structure and Conformation I. Molecular Modeling and Mechanics. Biopolymers 32: 11-21 1992.
  • V. Lounnas, B.M. Pettitt, L. Findsen & S. Subramaniam. A microscopic View of Protein Solvation. J. Phys. Chem. 96: 7157-7159, 1992.
  • S. Subramaniam, D. Tcheng, K. Hu, H. Raghavan & L. Rendell. Knowledge Engineering for Protein Structure and Motifs - Design of a Prototype System. IEEE Computer Society Journal (Proceedings of the Fourth International Conference on Software Engineering and Knowledge Engineering, Capri, Italy), 1992, pp. 420-434.
  • D. K. Tcheng and S. Subramaniam. Machine Learning Approaches to Protein Feature Prediction. Int. J. Neural Systems. 3: 183-193, 1992.
  • S. W. Chiu, L. K. Nicholson, M. T. Brenneman, S. Subramaniam, Q. Teng, J. A. McCammon, T.A. Cross and E. Jakobsson. Molecular Dynamics Computations and Solid State NMR of the Gramicidin Cation Channel. Biophys. J. 60: 974-978, 1991.
  • S. W. Chiu, E. Jakobsson, S. Subramaniam and J. A. McCammon. Time Correlation Analysis of Water Transport through Gramicidin Ion Channel. Biophys. J. 60: 273-285 1991.
  • P. H. Kussie, J. Anchin, S. Subramaniam, J. A. Glazel & D. S. Linthicum. Molecular modeling of a monoclonal antimorphine antibody. J. Immunology 146: 4248-4257 1991.
  • J. Anchin, S. Subramaniam and S. Linthicum. Structure and Characterization of an Anti-haloperidol Antibody. J. Mol. Recog. 4: 7-15, 1991.