Publications for Carlos Simmerling
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).
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16506755
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).
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16418268&query_hl=1&itool=pubmed_docsum
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.
http://portal.isiknowledge.com/portal.cgi/wos?Init=Yes&SID=A634LGAMEMmJbfanhA8
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.
http://portal.isiknowledge.com/portal.cgi/wos?Init=Yes&SID=A634LGAMEMmJbfanhA8
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
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16200636&query_hl=1&itool=pubmed_docsum
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.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16201812&query_hl=1&itool=pubmed_docsum
Roe, D., Hornak, V. and
Simmerling, C., “Folding Cooperativity in a Three-stranded ?-sheet Model”, J.
Mol. Biol., 352, 370-281 (2005)
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16095612&query_hl=1&itool=pubmed_docsum
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)
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15797218&query_hl=1&itool=pubmed_docsum
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)
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15657048&query_hl=1&itool=pubmed_docsum
Roitberg, A. and Simmerling,
C., “Foreword”, J. Mol. Graphics & Modeling, 22:317,
2004
http://portal.isiknowledge.com/portal.cgi/wos?Init=Yes&SID=A634LGAMEMmJbfanhA8
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
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14736233&query_hl=1&itool=pubmed_docsum
Hornak, V. and Simmerling, C., “Development of Softcore Potential Functions
for Overcoming Steric Barriers in MD”, J. Mol. Graphics & Modeling,
22: 403, 2004
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15099836&query_hl=1&itool=pubmed_docsum
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.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12784217&query_hl=1&itool=pubmed_docsum
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.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12236726&query_hl=1&itool=pubmed_docsum
Cui, G and Simmerling, C., ‘Conformational Heterogeneity Observed in Simulations
of a Pyrene-Substitued DNA’, J. Am. Chem. Soc., 124:12154,
2002.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12371855&query_hl=1&itool=pubmed_docsum
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
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11395498&query_hl=1&itool=pubmed_docsum
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
http://portal.isiknowledge.com/portal.cgi/wos?Init=Yes&SID=A634LGAMEMmJbfanhA8
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.
http://portal.isiknowledge.com/portal.cgi/wos?Init=Yes&SID=A634LGAMEMmJbfanhA8
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.
http://portal.isiknowledge.com/portal.cgi/wos?Init=Yes&SID=A634LGAMEMmJbfanhA8
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
http://portal.isiknowledge.com/portal.cgi/wos?Init=Yes&SID=A634LGAMEMmJbfanhA8
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
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7724538&query_hl=1&itool=pubmed_docsum
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)
http://portal.isiknowledge.com/portal.cgi/wos?Init=Yes&SID=A634LGAMEMmJbfanhA8