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Okur, A. and Simmerling, C., "Hybrid Explicit/Implicit Solvation Methods", Annual Reports in Computational Chemistry 2006, in press.
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., in press.
Wickstrom, L., Okur, A., Song, K., Hornak, V., Raleigh, D. and Simmerling, C., "", J. Mol. Biol., in press.
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, in press.
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).
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).
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.
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.
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., 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.
Roe, D., Hornak, V. and Simmerling, C., "Folding Cooperativity in a Three-stranded ?-sheet Model", J. Mol. Biol., 352, 370-281 (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)
Geney, R., Sun, L., Pera, P., Bernacki, R., Xia, R., Horwitz, S., Simmerling, C., and Ojima, I. "Use of the tubulin-bound paclitaxel conformation for structure-based rational drug design", Chemistry & Biology, 12, 339-348 (2005)
Kubatzky, K., Liu, W., Goldgraben, K., Simmerling, C., Steven O. Smith, S., and Constantinescu, S., 'Structural Requirements of the Extracellular To Transmembrane Domain Junction for Erythropoietin Receptor Function", J. Biol. Chem., 280, 14844-14854 (2005)
Roitberg, A. and Simmerling, C., "Foreword", J. Mol. Graphics & Modeling, 22:317, 2004
Cheng, X., Hornak, V. and Simmerling, C., "Improved Conformational Sampling through an Efficient Combination of Mean-Field Simulation Approaches". J. Phys. Chem. B, 108:426, 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
Hornak, V. and Simmerling, C., "Development of Softcore Potential Functions for Overcoming Steric Barriers in MD", J. Mol. Graphics & Modeling, 22: 403, 2004
Hornak, V. and Simmerling, C., "Generation of Accurate Protein Loop Conformations through Low-barrier Molecular Dynamics", Proteins: Struct. Func. Genet., 51:577,200314
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.
Simmerling, C., Strockbine, B and Roitberg, A., 'All-Atom Structure Prediction and Folding Simulations of a Stable Protein', J. Am. Chem. Soc, 124:11258, 2002.
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 ? 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 ??? Anomerization of Glucose', J. Am. Chem. Soc, 120:5771,1998.
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
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., Roitberg, A., Simmerling, C., Goldstein, R., Verkhivker, G., Li, H. and Ulitsky, A., 'MOIL- A Program for Simulation of Macromolecules', Computer Physics Communications, 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
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)
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)