Altobelli, G. & Subramaniam, S. (2000). Kinetics of association of anti-lysozyme monocional antibody D44.1 and hen-egg lysozyme. Biophysical Journal (in print).

Gibas, C.J., Jambeck, P., & Subramaniam, S. (2000). Continuum electrostatic methods applied to pH-dependent properties of antibody-antigen association. Methods, 20, 292-309.

Heggard, S., Gibas, C., & Subramaniam, S. (2000). Role of electrostatic network of residues in the enzymatic action of Rhizomucor miehei lipase family. Biochemistry, 39(11), 2921-2930.

Herrgard, S., Jambeck, P., Taylor, S., & Subramaniam, S. (2000). Domain architecture of C. elegans AKAP suggests a novel AKAP function. (submitted for publication).

Ramarathnam, R. & Subramaniam, S. (2000). A novel microarray strategy for detecting genes and pathways in microbes with unsequenced genomes. (submitted for publication).

Rojnuckarin, A., Livesay, D.R., & Subramaniam, S. (2000). Biomolecular reaction simulation using weighted ensemble brownian dynamics and the University of Houston Brownian Dynamics Program. Biophysical Journal, 79, 686-693.

Subramaniam, S. (2000). Phylogenomic analysis of the alpha proteasome gene family from early diverging eukaryotes. Journal of Molecular Evolution, (in print).

Viswanathan, M., Linthicum, D.S., & Subramaniam, S. (2000). Analysis of correlated motion in antibody combining sites from molecular dynamics simulation. Methods, 20, 362-371.

Zou, G., Skeetl, R.D., & Subramaniam, S. (2000). Biased brownian dynamics for rate constant calculation. Biophysical Journal, 79, 638-645.

Chiu, S.W., Jakobsson, E., Subramaniam, S., & Scott, H.L. (1999). Combined monte carlo and molecular dynamics simulation of fully hydrated dioleyl and palmitoyl-oleyl phoshatidylcholine lipid bilayers. Biophysical Journal, 77, 2462-2469.

Chiu, S.W., Subramaniam, S., & Jakobsson, E. (1999). Simulation study of gramicidin/lipid bilayer system in excess water and lipid. I. Structure of the molecular complex. Biophysical Journal, 76(4), 1929-38.

Chiu, S.W., Subramaniam, S., & Jakobsson, E. (1999). Simulation study of gramicidin/lipid bilayer system in excess water and lipid. II. Rates and mechanisms of water transport. Biophysical Journal, 76(4), 1939-50.

Clark, M., Scott, H.L., Jakobsson, E., & Subramaniam, S. (1999). Simulation parameters for liquid hydrocarbons. Journal of Computational Chemistry (in print).

Livesay, D., Linthicum, S., & Subramaniam, S. (1999) pH dependence of antibody-hapten association. Molecular Immunology, 36, 397-410.

Rojnuckarin, A. & Subramaniam, S. (1999). Knowledge-based interaction potentials for proteins. Proteins: Structure, Function and Genetics, 36, 54-67.

Wall, M.E., Subramaniam, S., & Phillips, Jr., G.N. (1999). Protein structure determination using a database of interatomic distance probabilities. Protein Science, 8, 2720-2727.

Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P.V., & Subramaniam, S. (1998). Analytical shape computing of macromolecules: l. Molecular area and volume through alpha shape. Proteins: Structure, Function, and Genetics, 33, 1-17.

Liang, J., Edelsbrunner, H., Fu, P., Sudhaker, P.V., & Subramaniam, S. (1998). Analytical shape computing of macromolecules: ll. Inaccessible cavities in proteins. Proteins: Structure, Function, and Genetics, 33, 18-29.

Rojnuckarin, A., Kim, S., & Subramaniam, S. (1998). Brownian dynamics simulations of protein folding: Access to milliseconds time scale and beyond. Proc. Natl. Acad. Sci. USA, 95(8), 4288-4292.

Scott, H.L., Jakobsson, E., & Subramaniam, S. (1998). Simulations of lipid membranes with atomic resolution. Computational Physics, 12(4), 328-333.

Sivasankar, S., Subramaniam, S., & Leckband, D. (1998). Direct molecular level measurements of the electrostatic properties of a protein surface. Proc. Natl. Acad. Sci. USA, 95(22), 12961-12966.

Subramaniam, S. (1998). The Biology Workbench – A seamless database and analysis environment for the biologist. Proteins: Structure, Function, and Genetics, 32, 1-2.

Xiong, J., Subramaniam, S., & Govindjee. (1998). A knowledge-based three dimensional model of the photosystem ll reaction center of Chlamydomonas reinhardtii. Photosynthesis Research, 56, 229-254.

Gibas, C. & Subramaniam, S. (1997). Knowledge-based design of a soluble bacteriorhodopsin. Protein Eng., 10(10), 1175-1190.

Gibas, C., Subramaniam, S., McCammon, J.A., Braden, B.C., & Polijak, R.J. (1997). pH dependence of antibody/lysozome complexication. Biochemistry, 36(50), 15599-15614.

Liang, J. & Subramaniam, S. (1997). Computation of molecular electrostatics with boundary element methods. Biophysical Journal, 73, 1830-1841.

Pappas, G. & Subramaniam, S. (1997). An evaluation of protein secondary structure predictions algorithms. In: Techniques in protein chemistry VIII. (D.R. Marshak, Ed.). Academic Press: San Diego, CA.

Gibas, C.J. & Subramaniam, S. (1996). Explicit solvent models in protein pKa calculations. Biophysical Journal, 71, 138-147.

Jakobsson, E., Subramaniam, S., & Scott, H.L. (1996). Strategic issues in molecular dynamics simulations of membranes: In: Biological Membranes. (K. Merz Jr. & B. Roux, Eds.) Birkhauser: Boston.

Mandal, C., Kingery, B.D., Anchin, J.M., Subramaniam, S., & Linthicum, D.S. (1996). ABGEN: A knowledge-based authomated approach for antibody structure modeling. Nature-Biotechnology, 14(3), 323-328.

Singh, C., Sankararamakrishnan, R., Subramaniam, S., & Jakobsson, E. (1996). Solvation, water permeation, and ionic selectivity of a putative model for the pore region of the voltage-gated sodium channel. Biophysical Journal, 71, 2276-2288.

Subramaniam, S., Tcheng, D.K., & Fenton, J.M. (1996). Knowledge-based methods for protein structure refinement and prediction. In: Proceedings of the Fourth International Conference on Intelligent Systems in Molecular Biology. (David J. States et al., Eds.) AAAI Press: Menlo Park, CA.

Viswanathan, M., Subramaniam, S., Pledger, D.W., Tetin, S.Y., & Linthicum, D.S. (1996). Modeling the structure of the combining site of an antisweet taste ligand monoclonal antibody NC10.14. Biopolymers, 39, 395-406.

Xiong, J., Subramaniam, S, & Govindjee. (1996). Modeling of the D1/D2 proteins and cofactors of the photosystem II reaction center: implications for herbicide and bicarbonate binding. Protein Science, 5, 2054-2073.

Chiu, S.W., Clark, M, Balaji, V., Subramaniam, S., Scott, H.L., & Jakobsson, E. (1995). Incorporation of surface tension into molecular dynamics simulation of an interface: A fluid phase lipid bilayer membrane. Biophysical Journal, 69, 1230-1245.

Ioerger, T.R., Rendell, L.A., & Subramaniam, S. (1995). Searching for representations to improve protein sequence fold-class prediction. Machine Learning, 21, 151-175.

Kozack, R.E., d’Mello, M.J., & Subramaniam, S. (1995). Computer modeling of electrostatic steering and orientational effects in antibody-antigen association. Biophysical Journal, 68, 807-814.

Tang, L., Ebrey, T.G., & Subramaniam, S. (1995). Sequences and structures of retinal proteins. Isr. J. Chem., 35, 193-209.

Viswanathan, M. Anchin, J.M., Droupadi, P.R., Mandal, C., Linthicum, D.S., & Subramaniam, S. (1995) Structural predictions of the binding site architecture for monoclonal antibody NC6.8 using computer-aided molecular modeling, ligand binding, and spectroscopy. Biophysical Journal, 69(3), 741-753.

Anchin, J.M., Mandal, C., Culberson, C., Subramaniam, S., & Linthicum, D.S. (1994). Computer-aided molecular modeling of the binding site architecture for eight monoclonal antibodies that bind a high potency guanidinium sweetener. Journal of Molecular Graphics, 12, 257-266.

Forsten, K.E., Kozack, R.E., Lauffenburger, D.A., & Subramaniam, S. (1994). Numerical solution of the nonlinear Poisson-Boltzmann equation for a membrane-electrolyte. Journal of Physical Chemistry, 98, 5580-5586.

Holst, M., Kozack, R.E., Saied, F., & Subramaniam, S. (1994). 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, 231-245.

Holst, M., Kozack, R.E., Saied, F., & Subramaniam, S. (1994). Protein electrostatics: Rapid multigrid-based Newton algorithm for solution of the full nonlinear Poisson-Boltzmann equation. Journal of Biomolecular Structure & Dynamics, 11(6), 1437-1445.

Reczko, M., Bohr, H., Subramaniam, S., Pamidinghantam, S., & Hatzigeorgiou, A. (1994). Fold-class prediction by neural network. In: Protein Structure by Distance Analysis. (H. Bohr & S. Brunak, Eds.). IOS Press: Amsterdam.

Slagle, S.P., Kozack, R.E., & Subramaniam, S. (1994). Role of electrostatics in antibody-antigen association: Anti-hen egg lysozyme/lysozyme complex (HyHEL-5/HEL). Journal of Biomolecular Structure & Dynamics, 12(2), 439-456.

Subramaniam, S. (1994). Protein structure prediction: past and present. In: Proetin structure by distance analysis. (H. Bohr & S. Brunak, eds.) IOS Press: Washington, DC.

Susnow, R., Schutt, C., Rabitz, H, & Subramaniam, S. (1994). Conformational study of dipeptides: A sensitivity analysis approach. Journal of Computational Chemistry, 15(9), 947-962.

Ioerger, T.R., Rendell, L., & Subramaniam, S. (1993). Constructive induction and protein tertiary structure prediction. Ismb, 1, 198-206.

Kozack, R. & Subramaniam, S. (1993). Brownian dynamics simulations of molecular recognition in an antibody-antigen system. Protein Science, 2, 915-926.

Bassolino-Klimas, D., Bruccoleri, R.E., & Subramaniam, S. (1992). Modeling the antigen combining site of an anti-dinitrophenyl antibody, ANO2. Protein Science, 1(11), 1465-1472.

Nell, L.J., McCammon, J.A., Subramaniam, S. (1992). Anti-insulin antibody structure and conformation. I. Molecular modeling and mechanics of an insulin antibody. Biopolymers, 32(1), 11-21.

Rodgers, K.R., Su, C., Subramaniam, S., & Spiro, T.G. (1992). Hemoglobin R® T structural dynamics from simultaneous monitoring of tyrosine and tryptophan time-released UV resonance raman signals. Journal of the American Chemical Society, 114(10), 3697-3709.

Subramaniam, S., Tcheng, D.K., Hu, K., Ragavan, H., & Rendell, L.A. (1992). Knowledge engineering for protein structure and motifs: Design of a prototype system. In: Proceedings of the Fourth International Conference on Software Engineering and Knowledge Engineering. IEEE Computer Society Press: Los Alamitos, CA.

Tcheng, D.K. & Subramaniam, S. (1992). Machine approaches to protein feature prediction. International Journal of Neural Systems, 3, 183-193.

Anchin, J.M., Subramaniam, S., & Linthicum, D.S. (1991). Binding of the neuroleptic drug haloperidol to a monoclonal antibody: Refinement of the binding site molecular model using canonical structures. Journal of Molecular Recognition, 4(1), 7-15.

Chiu, S.W., Jakobsson, E., Subramaniam, S., & McCammon, J.A. (1991). Time-correlation analysis of simulated water motion in flexible and rigid gramicidin channels. Biophysical Journal, 60(1), 273-285.

Chiu, S.W., Nicholson, L.K., Brenneman, M.T., Subramaniam, S., Teng, Q., McCammon, J.A., Cross, T.A., & Jakobsson, E. (1991). Molecular dynamics computations and solid state nuclear magnetic resonance of the gramicidin cation channel. Biophysical Journal, 60(4), 974-978.

Kussie, P.H., Anchin, J.M., Subramaniam, S., & Glasel, J.A. (1991). Analysis of the binding site architecture of monoclonal antibodies to morphine by using competitive ligand binding and molecular modeling. Journal of Immunology, 146(12), 4248-4257.

Chiu, S.W., Subramaniam, S., Jakobsson, E., & McCammon, J.A. (1989). Water and polypeptide conformations in the gramicidin channel. A molecular dynamics study. Biophysical Journal, 56(2), 253-261.