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Song, K., Hornak, V., de los Santos, C., Grollman, A. and Simmerling, C., “Molecular Mechanics Parameters for the FapydG DNA lesion”, J. Comput. Chem., in press

Wickstrom, L., Bi, Y., Hornak, V., Raleigh, D. and Simmerling, C., “Reconciling the Solution and X-ray Structures of the Villin Headpiece Helical Subdomain: Molecular Dynamics Simulations and Double Mutant Cycles Reveal a Stabilizing Cation-Pi Interaction”, Biochemistry, 46:3624-3634 (2007) (listed as “Hot Article” by Biochemistry)

Roitberg, A., Okur, A. and Simmerling, C., “Coupling of Replica Exchange Simulations to a non-Boltzmann structure reservoir”, J. Phys. Chem. B, 111:2415-2418 (2007)

Roe, D., Okur, A., Wickstrom, L., Hornak, V. and Simmerling, C., “Secondary Structure Bias in Generalized Born Solvent Models: Comparison of Conformational Ensembles and Free Energy of Solvent Polarization from Explicit and Implicit Solvation”, J. Phys. Chem. B, 111:1846-1857 (2007)

Hornak, V. and Simmerling, C., “Targeting structural flexibility in HIV-1 protease inhibitor binding”, Drug Discovery Today, 12:132-138 (2007)

Okur, A., Roe, D., Cui, G., Hornak, V. and Simmerling, C., “Improving Convergence of Replica Exchange Simulations through Coupling to a High Temperature Structure Reservoir”, J. Chem. Theory & Comput., 3:557-568 (2007)

Mongan, J., Simmerling, C., McCammon, J. A., Case, D.and Onufriev, A., Generalized Born model with a simple, robust molecular volume correction, J. Chem. Theory & Comput., 3:156-169 (2007)

Hornak, V.; Okur, A., Rizzo, R. and Simmerling, C., “HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations”, Proc. Nat. Acad. Sci. USA, 103:915-920 (2006).

Hornak, V.; Okur, A., Rizzo, R. and Simmerling, C., “HIV-1 Protease Flaps Spontaneously Close to the Correct Structure in Simulations Following Manual Placement of an Inhibitor into the Open State”, J. Am. Chem. Soc., 128: 2812 (2006).

Layten, M., Hornak, V. and Simmerling, C., The open structure of a multi drug resistant HIV-1 protease is stabilized by crystal packing contacts, J. Am. Chem. Soc., 128: 13360-13361 (2006)

Rafi, S., Novichenok, P., Kolappan, S., Zhang, X., Strattor, C., Rawat, R., Kisker, C., Simmerling, C. and Tonge, P., “Structure of Acyl Carrier Protein Bound to FabI, the FASII Enoyl Reductase from Escherichia Coli, J. Biol. Chem., 281: 39285-39293 (2006)

Wickstrom, L., Okur, A., Song, K., Hornak, V., Raleigh, D. and Simmerling, C., “The Unfolded State of the Villin Headpiece Helical Subdomain: Computational Studies of the Role of Locally Stabilized Structure”, J. Mol. Biol., 360:1094-1107 (2006).

Song, K., Hornak, V., de los Santos, C., Grollman, A. and Simmerling, C., Computational analysis of the binding mode of 8-oxo-guanine to formamidopyrimidine-DNA glycosylase, Biochemistry, 45:10886-10894 (2006)

Rafi, S., Cui, G., Song, K., Cheng, X., Tonge, P. and Simmerling, C., “Insight through MM-PBSA Calculations into the Binding Affinity of Triclosan and Three Analogs for FabI, the E. Coli Enoyl Reductase”, J. Med. Chem., 49:4574-4580 (2006).

Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A. and Simmerling, C., “Comparison of multiple Amber force fields and development of improved protein backbone parameters”, Proteins: Structure, Function and Genetics, 3:712-725 (2006).

Geney, R., Layten, M., Gomperts, R., Hornak, V. and Simmerling, C., “Investigation of salt bridge stability in a Generalized Born solvent model”, J. Chem. Theory Comput., 2:115, 2006.

Okur, A., Wickstrom, L., Layten, M., Geney, R., Song, K., Hornak, V. and Simmerling, C., “Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model”, J. Chem. Theory Comput., 2:420, 2006.

Kelso, C. and Simmerling, C., “Enhanced Sampling Methods for Simulation of Nucleic Acids”, in Computational Studies of DNA and RNA, J. Sponer and F. Lankas (Editors), Springer Publishers, 147-168 (2006).

Okur, A. and Simmerling, C., “Hybrid Explicit/Implicit Solvation Methods”, Annual Reports in Computational Chemistry, 2:97-109 (2006).

Roe, D., Hornak, V. and Simmerling, C., “Folding Cooperativity in a Three-stranded -sheet Model”, J. Mol. Biol., 352, 370-281 (2005)

Cheng, X., Kelso, C., Hornak, V., de los Santos, C., Grollman, A. and Simmerling, C., “Dynamic Behavior of DNA Base Pairs Containing 8-oxoguanine”, J. Am. Chem. Soc., 127:13906, 2005.

Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J., “The Amber biomolecular simulation program”, J. of Comput. Chem. 26:1668, 2005

Cheng, X., Cui, G., Hornak, V. and Simmerling, C., “Modified Replica Exchange Simulation Methods for Local Structure Refinement”. J. Phys. Chem. B, 109, 8220-8230 2005

Cheng, X., Hornak, V. and Simmerling, C., “Improved Conformational Sampling through an Efficient Combination of Mean-Field Simulation Approaches”. J. Phys. Chem., 108:426, 2004

Hornak, V. and Simmerling, C., “Development of Softcore Potential Functions for Overcoming Steric Barriers in MD”, J. Mol. Graphics & Modeling, 22: 403, 2004

Sivaraman, S., Sullivan, T., Johnson. F., Novichenok, P., Cui, G., Simmerling, C., Johnson, F. and Tonge, P. “Inhibition of the Bacterial Enoyl Reductase FabI by Triclosan: A Structure-Reactivity Analysis of FabI Inhibition by Triclosan Analogs”, J. Med. Chem., 47:509, 2004

Roitberg, A. and Simmerling, C., “Foreword”, J. Mol. Graphics & Modeling, 22:317, 2004

Okur, A., Strockbine, B., Hornak, V. and Simmerling, C., ‘Using PC Clusters to Evaluate the Transferability of Molecular Mechanics Force Fields for Proteins”, J. Comput. Chem., 24:21, 2003.

Hornak, V. and Simmerling, C., “Generation of Accurate Protein Loop Conformations through Low-barrier Molecular Dynamics”, Proteins: Struct. Func. Genet., 51:577,2003

Cui, G and Simmerling, C., ‘Conformational Heterogeneity Observed in Simulations of a Pyrene-Substitued DNA’, J. Am. Chem. Soc., 124:12154, 2002.

Shewmaker, F., Maskos, K., Simmerling, C. and Landry, S. J. ‘The Disordered Mobile Loop of GroES Folds into a Defined b Hairpin upon Binding GroEL’ J. Biol. Chem., 276:33, 2001

Simmerling, C., Lee, M.R, Ortiz, AR., Kolinski, A., Skolnick, J., Kollman, P.A., ‘Combining MONSSTER and LES/PME to Predict Protein Structure from Amino Acid Sequence: Application to the Small Protein CMTI-I’, J. Am. Chem. Soc., 122:8392 (2000)

Simmerling, C., Miller, J. L., and Kollman, P., ‘Combined Locally Enhanced Sampling and Particle Mesh Ewald as a Strategy to Locate the Experimental Structure of a Non-helical Nucleic Acid’, J. Am. Chem. Soc, 120:7149 (1998)

Simmerling, C., Fox, T. and Kollman, P., ‘The Use of Locally Enhanced Sampling in Free Energy Calculations: Testing and Application to the aàb Anomerization of Glucose’, J. Am. Chem. Soc, 120:5771 (1998)

Case, D.A., Pearlman, D.A., Caldwell, J.A., Cheatham, T.E., Ross, W.S., Simmerling, C.L., Darden, T.A., Merz, K.M., Stanton, R.V., Cheng, A.L., Vincent, J.J., Crowley, M., Ferguson, D.M., Radmer, R.J., Seibel, G.L., Singh, U.C., Weiner, P.K. and Kollman, P.A., AMBER 5, University of California, San Francisco (1997)

Elber, R., Mohanty, D. and Simmerling, C. “Dynamics of Peptide Folding” in Classical and Quantum Dynamics in Condensed Phase Simulations, B. Berne et. al. (eds.) World Scientific, Singapore (1998)

Elber, R., Roitberg, A., Simmerling, C., Goldstein, R., Verkhivker, G., Li, H. and Ulitsky, A., ‘MOIL- A Program for Simulation of Macromolecules’, Comp. Phys. Comm., 91:159 (1995)

Simmerling, C., Elber, R. and Zhang, J., ‘MOIL-View: A Program for Visualization of Structure and Dynamics of Biomolecules and STO: a Program for Computing Stochastic Paths’, in Modeling of Biomolecular Structures and Mechanisms, A. Pullman et al. (eds.) Kluwer Acad. Publishers, Netherlands (1995)

Simmerling, C. and Elber, R., ‘Computer Determination of Peptide Conformations in Water: Different Roads to Structure’, Proc. Nat. Acad. Sci. USA, 92:3190 (1995)

Simmerling, C. and Elber, R., ‘Hydrophobic “Collapse” in a Cyclic Hexapeptide: Computer Simulations of CHDLFC and CAAAAC in Water’, J. Am. Chem. Soc., 16:2534 (1994)

Elber, R., Roitberg, A., Simmerling, C., Goldstein, R., Verkhivker, G. and Li, H., ‘MOIL- A Molecular Dynamics Program with Emphasis on Conformational Searches and Reaction Path Calculations in Large Biological Molecules’ in Statistical Mechanics, Protein Structure and Protein-Substrate Interactions, S Doniach (ed.), Plenum Press, NY (1994)