Publications

Characterization of Biomolecular Helices and Their Complementarity Using Geometric Analysis
Hauser Kevin; He Yiqing; Garcia-Diaz Miguel; Simmerling Carlos; Coutsias Evangelos A. Journal of Chemical Information and Modeling, 2017,
DOI: 10.1021/acs.jcim.6b00721

DNA Deformation-Coupled Recognition of 8‑Oxoguanine: Conformational Kinetic Gating in Human DNA Glycosylase
Haoquan Li, Anton V. Endutkin, Christina Bergonzo, Lin Fu, Arthur Grollman, Dmitry O. Zharkov, and Carlos Simmerling, Journal of the American Chemical Society, 2017, 139 (7), 2682-2692
DOI: 10.1021/jacs.6b11433
PMCID: PMC5321822

Experimental and Computational Analysis of Protein Stabilization by Gly-to-D-Ala Substitution: A Convolution of Native State and Unfolded State Effects
Zou, Junjie; Song, Benben; Simmerling, Carlos; Raleigh, Daniel, Journal of the American Chemical Society, 2016, 138 (48), 15682–15689
DOI: 10.1021/jacs.6b09511

Selectivity of Pyridone-and Diphenyl Ether-Based Inhibitors for the Yersinia pestis FabV Enoyl-ACP Reductase FabV]
Neckles, C., Pschibul, A., Lai, C.-T, Hirschbeck, M., Kuper, J., Davoodi, S., Zou, J., Liu, N., Pan P., Shah, S., Daryaee, F., Bommineni, G., Lai, C., Simmerling, C., Kisker, C. Tonge, P., Biochemistry, 2016, 55(21), 2992–3006
DOI: 10.1021/acs.biochem.5b01301
PMCID: PMC4887296

Advances in free-energy-based simulations of protein folding and ligand binding]
Perez, A., Morrone, J. A., Simmerling, C. Dill, K. A., Current Opinion in Structural Biology, 2016, 36, 25–31
DOI: 10.1016/j.sbi.2015.12.002
PMCID: PMC4785060

A human transcription factor in search mode
Hauser, K., Essuman, B., He, Y., Coutsias, E., Garcia-Diaz, M., Simmerling, C., Nucleic Acids Research, 2016, 44(1), 63–74
DOI: 10.1093/nar/gkv1091
PMCID: PMC4705650

A Dynamic Checkpoint in Oxidative Lesion Discrimination by Formamidopyrimidine–DNA Glycosylase
Li, H., Endutkin, A., Bergonzo, C., Grollman, A.; Campbell, A., de los Santos, C., Zharkov, D., Simmerling, C., Nucleic Acids Research, 2015,44(2), 683-94
DOI:10.1093/nar/gkv1092
PMCID: PMC4737139

Base flipping by MTERF1 can accommodate multiple conformations and occurs in a stepwise fashion
Byrnes, J., Hauser, K., Mejia, E.,, Norona, L.,Simmerling, C., Garcia-Diaz, M.,Journal of Molecular Biology, 2015, 428(12), 2542-56
DOI: 10.1016/j.jmb.2015.10.021
PMCID: PMC4851923

A grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations
Perez, A., MacCallum, JL., Brini, E., Simmerling, C., Dill, KA, Journal of Chemical Theory and Computation, 2015, 11 (10), 4770–4779
DOI: 10.1021/acs.jctc.5b00662
PMCID: PMC4813323

Rational modulation of the induced-fit conformational change for slow-onset inhibition in M. tuberculosis InhA
Lai, C-T., Li, H; Yu, W., Shah, S., Bommineni, G., Perrone, V., Garcia-Diaz, M., Tonge, P., Simmerling, C., Biochemistry, 2015, 54 (30), 4683-4691
DOI: 10.1021/acs.biochem.5b00284
PMCID: PMC4805124

ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB
Maier, J., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K., Simmerling, C., Journal of Chemical Theory and Computation, 2015, 11 (8), 3696-3713
DOI: 10.1021/acs.jctc.5b00255
PMCID: PMC4821407

Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins
Nguyen, H., Pérez, A., Bermeo, S., Simmerling, C., Journal of Chemical Theory and Computation, 2015, 11 (8), 3714-3728
DOI: 10.1021/acs.jctc.5b00271
PMCID: PMC4805114

Active destabilization of base pairs by a DNA glycosylase wedge initiates damage recognition
Kuznetsov, N. A., Bergonzo, C., Campbell, A. J., Li, H., Mechetin, G. V., de los Santos, C., Grollman, A. P., Fedorova, O. S., Zharkov, D. O., Simmerling, C., Nucleic Acids Research, 2015, 43 (1), 272-281
DOI: 10.1093/nar/gku1300
PMCID: PMC4288190

Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent
Nguyen, H., Maier, J., Huang, H., Perrone, V., Simmerling, C., Journal of the American Chemical Society, 2014, 136 (40), 13959-13962
DOI: 10.1021/ja503277669
PMCID: PMC4195377

The Role of Select Subtype Polymorphisms on HIV-1 Protease Conformational Sampling and Dynamics
Huang, X., Britto, M., Kear, J., Boone, C., Rocca, J., Simmerling, C., McKenna, R., Bieri, M., Gooley, P., Dunn, B. and Fanucci, G., Journal of Biological Chemistry, 2014, 289, 17203-17214
DOI: 10.1074/jbc.M114.571836
PMCID: PMC4059161

A structural and energetic model for the slow-onset inhibition of the Mycobacterium tuberculosis enoyl-ACP reductase InhA
Li, H.; Lai, C.; Pan, P.; Yu, W.; Liu, N.; Bommineni, G.; Garcia-Diaz, M.; Simmerling, C. .; Tonge, PJ., ACS Chemical Biology, 2014, 9, (4), 986–993
DOI: 110.1021/cb400896g
PMCID: PMC4059161

Time-Dependent Diaryl Ether Inhibitors of InhA: Structure–Activity Relationship Studies of Enzyme Inhibition, Antibacterial Activity, and in vivo Efficacy
Pan, P., Knudson, SE, Bommineni, GR, Li, H., Lai, C., Liu, N., Garcia-Diaz, M., Simmerling, C., Patil, SS, Slayden, RA, Tonge, PJ., ChemMedChem, 2014, 9, (4), 776–791
DOI: 10.1002/cmdc.201300429
PMCID: PMC4126670

Ultrafast Structural Dynamics of BlsA, a Photoreceptor from the Pathogenic Bacterium Acinetobacter baumannii
Brust, R., Haigney, A., Lukacs, A., Gil., A., Hossain, S., Addison, K., Lai, CT, Towrie, M., Greetham, GM, Clark, IP, Illarionov, B., Bacher, A., Kim, RR, Fischer, M., Simmerling, C., Meech, SR and Tonge, PJ,Journal of Physical Chemistry Letter, 2014, 5, 220-224
DOI: 10.1021/jz4023738
PMCID: PMC3977573

Improved Generalized Born Solvent Model Parameters for Protein Simulations
Nguyen, H., Roe, D. R., Simmerling, C., Journal of Chemical Theory and Computation, 2013, 9 (4), 2020-2034
DOI: 10.1021/ct3010485
PMCID: PMC4361090

Development of an Automated Event Detection Algorithm for HIV-1 Protease’s Flap Backbone Dihedral Change
Gee, J., Weaver, E., Shang, Y., Simmerling, C., The Journal of Experimental Secondary Science, 2013, 2(4)

Thiolactomycin-based beta-Ketoacyl-AcpM Synthase A (KasA) Inhibitors: Fragment-Based Inhibitor Discovery Using Transient One-Dimensional Nuclear Overhauser Effect NMR Spectroscopy
Kapilashrami, K; Bommineni, G; Machutta, C; Kim, P; Lai, C; Simmerling, C; Picart, F; Tonge, PJ, Journal of Biological Chemistry, 2013, 288 , 6045-6052
DOI: 10.1074/jbc.M112.414516
PMCID: PMC3585043


Backbone 1H, 13C, and 15N Chemical Shift Assignment for HIV-1 Protease Subtypes and Multi-Drug Resistant Variant MDR 769
Huang, X., Veloro, A., De Vera, I., Rocca, J., Simmerling, C., Dunn, B. and Fanucci, G., Biomolecular NMR Assignments, 2013, 7(2), 199-202
DOI: 10.1007/s12104-012-9409-7
PMCID: PMC3518686

Inhibitor-Induced Conformational Shifts and Ligand-Exchange Dynamics for HIV-1 Protease Measured by Pulsed EPR and NMR Spectroscopy
Huang, X; de Vera, IMS; Veloro, AM; Blackburn, ME; Kear, JL; Carter, JD; Rocca, JR; Simmerling, C; Dunn, BM; Fanucci, GE, Journal of Physical Chemistry B, 2012, 116, 14235-14244
DOI: 10.1021/jp308207h
PMCID: PMC3709468

Structural Transitions of Transmembrane Helix 6 in the Formation of Metarhodopsin I
Eilers M, Goncalves J, Ahuja S, Kirkup C, Hirshfeld A, Simmerling C., Reeves P, Sheves M, Smith S., Journal of Physical Chemistry B, 2012, 116, 10477-10489
DOI: 10.1021/jp3019183
PMCID: PMC3428503

Molecular dynamics applied in drug discovery: the case of HIV-1 protease
Shang, Y. and Simmerling, C., Computational Drug Discovery and Design, 2012, 819, 527-549
DOI: 10.1007/978-1-61779-465-0_31

CoA Adducts of 4-Oxo-4-phenylbut-2-enoates: Inhibitors of MenB from the M. tuberculosis Menaquinone Biosynthesis Pathway
Li, x., Liu, N., Zhang, H., Knudson, S., Li, H., Lai, C., Simmerling, C., Slayden, R and Tonge, P., ACS Medicinal Chemistry Letters, 2011, 2, 818-823
DOI: 10.1021/ml200141e
PMCID: PMC3259734

Energetic Preference of 8-oxoG Eversion Pathways in a DNA Glycosylase
Bergonzo, C., Campbell, A., de los Santos, C., Grollman, A and Simmerling, C., Journal of the American Chemical Society, 2011, 133, 14504–14506
DOI: 10.1021/ja205142d
PMCID: PMC3173571

An Overview of String-Based Path Sampling Methods
Bergonzo, C. and Simmerling, C., Annual Report in Computational Chemistry, 2011, 7, 89-97

Improving the description of salt bridge strength and geometry in a Generalized Born model
Shang, Y., Nguyen, H., Wickstrom, L., Okur, A. and Simmerling, C., Journal of Molecular Graphics and Modelling., 2011, 29, 676-684
DOI: 10.1016/j.jmgm.2010.11.013
PMCID: PMC3390179


Synthesis and Molecular Modeling of a Nitrogen Mustard DNA Interstrand Crosslink
Guainazzi, A., Campbell, A. J., Angelov, T., Simmerling, C., Schärer, O. D.
Chemistry A European Journal, 2010, 16, 12100-12103
DOI: 10.1002/chem.201002041
PMCID: PMC4870935

Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber
Luchko, T., Gusarov, S., Roe, D., Simmerling, C., Case, D., Tuszynski, J. and Kovalenko, A.
Journal of Chemical Theory and Computation, 2010, 6, 607-624
DOI: 10.1021/ct900460m
PMCID: PMC2861832

Slow onset inhibition of bacterial & β-ketoacyl-ACP synthases by thiolactomycin
Machutta, C., Gopal, B., Luckner, S., Kapilashrami, K., Ruzsicska, B., Simmerling, C., Kisker, C., and Tonge, P.
J. Biol. Chem., 2010, 285, 6161-6169
DOI: 10.1074/jbc.M109.077909
PMCID: PMC2825411

An Improved Reaction Coordinate for Nucleic Acid Base Flipping Studies
Song, K., Campbell, A., Bergonzo, C., de los Santos, C., Grollman, A., Simmerling, C.
Journal of Chemical Theory and Computation, 2009, 5 (11), 3105-3113
DOI: 10.1021/ct9001575

A Partial Nudged Elastic Band Implementation for Use with Large or Explicitly Solvated Systems
Bergonzo, C., Campbell, A., Walker, R., Simmerling, C.
International Journal of Quantum Chemistry, 2009, 109, 3781-3790
DOI: 10.1002/qua.22405
PMCID: PMC2818052

Studies of Drug Resistance and the Dynamic Behavior of HIV-1 Protease through Molecular Dynamics Simulations
Ding, F. and Simmerling, C.
Drug Design: Structure and Ligand-Based Approaches, Cambridge University Press, 87-97, 2010

Discovery in Basic Energy Sciences: The Role Of Computing At The Extreme Scale
Gallia, G., Dunning, T., Head-Gordon, M., Kotliar, G., Grossman, J., Ho, K., Chou, M., Dupois, M., Asta, M. and Simmerling, C.
DOE Workshop Report, 2010

Drug Pressure Selected Mutations in HIV-1 Protease Alter Flap Conformations
Galiano, L., Ding, F., Veloro, A., Blackburn, M., Simmerling, C.and Fanucci, G.
<i>Journal of the American Chemical Society
, 2009, 131 (2), 430-431
DOI: 10.1021/ja807531v
PMCID: PMC2705922

Recent Advances in the Study of the Bioactive Conformation of Taxol
Sun, L., Simmerling, C. and Ojima, I.
ChemMedChem, 2009, 4, 719-731
DOI: 10.1002/cmdc.200900044
PMCID: PMC3072276

Evaluating the Performance of the FF99SB Force Field Based on NMR Scalar Coupling Data
Wickstrom, L., Okur, A. and Simmerling, C.
Biophysical Journal, 2009, 97 (3), 853-856
DOI: 10.1016/j.bpj.2009.04.063
PMCID: PMC2718158

Structural Insights for Designed Alanine-rich Helices: Comparing NMR Helicity Measures and Conformational Ensembles from Molecular Dynamics Simulation
Song, K., Stewart, J., Fesinmeyer, M. Andersen, N., Simmerling, C.
Biopolymers, 2008, 89, 747-760
DOI: 10.1002/bip.21004
PMCID: PMC3816200

Solution Structure of HIV-1 Protease Flaps Probed by Comparison of Molecular Dynamics Simulation Ensembles and EPR Experiments
Ding, F., Layten, M., Simmerling, C.
Journal of the American Chemical Society, 2008, 130 (23), 7184-7185
DOI: 10.1021/ja800893d
PMCID: PMC3390170

Evaluation of salt bridge structure and energetics in peptides using explicit, implicit and hybrid solvation models
Okur, A., Wickstrom, L. and Simmerling, C.
Journal of Chemical Theory and Computation, 2008, 4 (3), 488-498
DOI: 10.1021/ct7002308

Molecular simulations reveal a common binding mode for glycosylase binding of oxidatively damaged DNA lesions
Song, K., Kelso, C., de los Santos, C., Grollman, A. and Simmerling, C.
Journal of the American Chemical Society, 2007, 129 (47), 14536-14537
DOI: 10.1021/ja075128w
PMCID:PMC4814714

Molecular Mechanics Parameters for the FapydG DNA lesion
Song, K., Hornak, V., de los Santos, C., Grollman, A. and Simmerling, C.
Journal of Computational Chemistry, 2007, 29, 17-23
DOI: 10.1002/jcc.20625
PMCID:PMC4226240

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
Wickstrom, L., Bi, Y., Hornak, V., Raleigh, D. and Simmerling, C.
Biochemistry, 2007, 46 (12), 3624-3634
DOI: 10.1021/bi061785+
PMCID: PMC4822197

Coupling of Replica Exchange Simulations to a non-Boltzmann structure reservoir
Roitberg, A., Okur, A. and Simmerling, C.
Journal of Physical Chemistry B, 2007, 111 (10), 2415-2418
DOI: 10.1021/jp068335b
PMCID: PMC4819981

Secondary Structure Bias in Generalized Born Solvent Models: Comparison of Conformational Ensembles and Free Energy of Solvent Polarization from Explicit and Implicit Solvation
Roe, D., Okur, A., Wickstrom, L., Hornak, V. and Simmerling, C.
Journal of Physical Chemistry B, 2007, 111 (7), 1846-1857
DOI: 10.1021/jp066831u
PMCID: PMC4810457

Targeting structural flexibility in HIV-1 protease inhibitor binding
Hornak, V. and Simmerling, C.
Drug Discovery Today, 2007, 12 (3-4), 132-138
DOI: 10.1016/j.drudis.2006.12.011
PMCID: PMC4767006

Improving Convergence of Replica Exchange Simulations through Coupling to a High Temperature Structure Reservoir
Okur, A., Roe, D., Cui, G., Hornak, V. and Simmerling, C.
Journal of Chemical Theory and Computation, 2007, 3 (2), 557-568
DOI: 10.1021/ct600263e

Generalized Born model with a simple, robust molecular volume correction
Mongan, J., Simmerling, C., McCammon, J. A., Case, D.and Onufriev, A.
Journal of Chemical Theory and Computation, 2007, 3 (1), 156-169
DOI: 10.1021/ct600085e
PMCID: PMC2975579

HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations
Hornak, V., Okur, A., Rizzo, R. and Simmerling, C.
Proceedings of the National Academy of Sciences of the United States of America, 2006, 103 (4), 915-920
DOI: 10.1073/pnas.0508452103
PMCID: PMC1347991

HIV-1 Protease Flaps Spontaneously Close to the Correct Structure in Simulations Following Manual Placement of an Inhibitor into the Open State
Hornak, V.; Okur, A., Rizzo, R. and Simmerling, C.
Journal of the American Chemical Society, 2006, 128 (9), 2812-2813
DOI: 10.1021/ja058211x
PMCID: PMC2555982

Simulating HIV-1 Protease at its Most Vulnerable Instant
Simmerling, C. and Gomperts, R.
Scientific Computing, 2006, 7, 32-34

The open structure of a multi drug resistant HIV-1 protease is stabilized by crystal packing contacts
Layten, M., Hornak, V. and Simmerling, C.
Journal of American Chemical Society , 2006, 128 (41), 13360-13361
DOI: 10.1021/ja065133k
PMCID: PMC2532084

Structure of Acyl Carrier Protein Bound to FabI, the FASII Enoyl Reductase from Escherichia Coli
Rafi, S., Novichenok, P., Kolappan, S., Zhang, X., Strattor, C., Rawat, R., Kisker, C., Simmerling, C. and Tonge, P.
Journal of Biological Chemistry , 2006 , 281 (51), 39285-39293
DOI: 10.1074/jbc.M608758200
PMCID: PMC4819000

The Unfolded State of the Villin Headpiece Helical Subdomain: Computational Studies of the Role of Locally Stabilized Structure
Wickstrom, L., Okur, A., Song, K., Hornak, V., Raleigh, D. and Simmerling, C.
Journal of Molecular Biology , 2006, 360 (5), 1094-1107
DOI: 10.1016/j.jmb.2006.04.070
PMCID: PMC4805113

Computational analysis of the binding mode of 8-oxo-guanine to formamidopyrimidine-DNA glycosylase
Song, K., Hornak, V., de los Santos, C., Grollman, A. and Simmerling, C.
Biochemistry , 2006 , 45 (36), 10886-10894
DOI: 10.1021/bi060380m

Insight through MM-PBSA Calculations into the Binding Affinity of Triclosan and Three Analogs for FabI, the E. Coli Enoyl Reductase
Rafi, S., Cui, G., Song, K., Cheng, X., Tonge, P. and Simmerling, C.
Journal of Medicinal Chemistry, 2006 , 49 (15), 4574-4580
DOI: 10.1021/jm060222t

Comparison of multiple Amber force fields and development of improved protein backbone parameters
Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A. and Simmerling, C.
Proteins: Structure, Function and Bioinformatics , 2006 , 3 (3), 712-725
DOI: 10.1002/prot.21123
PMCID: PMC4805110

Investigation of salt bridge stability in a Generalized Born solvent model
Geney, R., Layten, M., Gomperts, R., Hornak, V. and Simmerling, C.
Journal of Chemical Theory and Computation, 2006 , 2 (1), 115-127
DOI: 10.1021/ct050183l

Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model
Okur, A., Wickstrom, L., Layten, M., Geney, R., Song, K., Hornak, V. and Simmerling, C.
Journal of Chemical Theory and Computation, 2006 , 2 (2), 420-433
DOI: 10.1021/ct050196z

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

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

Structural Requirements of the Extracellular To Transmembrane Domain Junction for Erythropoietin Receptor Function
Kubatzky, K., Liu, W., Goldgraben, K., Simmerling, C., Steven O. Smith, S., and Constantinescu, S.
Journal of Biological Chemistry , 2005 , 280 (15), 14844-14854
DOI: 10.1074/jbc.M411251200

Use of the tubulin-bound paclitaxel conformation for structure-based rational drug design
Geney, R., Sun, L., Pera, P., Bernacki, R., Xia, R., Horwitz, S., Simmerling, C., and Ojima, I.
Chemistry and Biology , 2005 , 12 (3), 339-348
DOI: 10.1016/Chemistry and Biology.2005.01.004

Folding Cooperativity in a Three-stranded beta-sheet Model
Roe, D., Hornak, V. and Simmerling, C.
Journal of Molecular Biology, 2005, 352 (2), 370-381
DOI: 10.1016/j.jmb.2005.07.036
PMCID: PMC4805115

Dynamic Behavior of DNA Base Pairs Containing 8-oxoguanine
Cheng, X., Kelso, C., Hornak, V., de los Santos, C., Grollman, A. and Simmerling, C.
Journal of American Chemical Society, 2005 , 127 (40), 13906-13918
DOI: 10.1021/ja052542s

The Amber biomolecular simulation program
Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J.
Journal of Computational Chemistry, 2005 , 26 , 1668-

Modified Replica Exchange Simulation Methods for Local Structure Refinement
Cheng, X., Cui, G., Hornak, V. and Simmerling, C.
Journal of Physical Chemistry B, 2005, 109 (16), 8220-8230
DOI: 10.1021/jp045437y
PMCID: PMC4805125
DOI: 10.1021/jp045437y

Improved Conformational Sampling through an Efficient Combination of Mean-Field Simulation Approaches
Cheng, X., Hornak, V. and Simmerling, C.
Journal of Physical Chemistry, 2004 , 108 (1), 426-437
DOI: 10.1021/jp034505y

Development of Softcore Potential Functions for Overcoming Steric Barriers in MD
Hornak, V. and Simmerling, C.
Journal of Molecular Graphics and Modelnig , 2004 , 22 (5), 405-413
DOI: 10.1016/j.jmgm.2003.12.007

Inhibition of the Bacterial Enoyl Reductase FabI by Triclosan: A Structure-Reactivity Analysis of FabI Inhibition by Triclosan Analogs
Sivaraman, S., Sullivan, T., Johnson. F., Novichenok, P., Cui, G., Simmerling, C., Johnson, F. and Tonge, P.
Journal of Medicinal Chemistry , 2004 , 47 (3), 509-518
DOI: 10.1021/jm030182i

Foreword: Conformational Sampling Special Issue
Roitberg, A. and Simmerling, C.
Journal of Molecular Graphics and Modeling, 2004, 22 (5), 317
DOI: 10.1016/j.jmgm.2004.03.015

Using PC Clusters to Evaluate the Transferability of Molecular Mechanics Force Fields for Proteins
Okur, A., Strockbine, B., Hornak, V. and Simmerling, C.
Journal of Computational Chemistry , 2003 , 24 (1), 21-31
DOI: 10.1002/jcc.10184

Generation of Accurate Protein Loop Conformations through Low-barrier Molecular Dynamics
Hornak, V. and Simmerling, C.
Proteins: Structure, Function, Genetics, 2003 , 51 (4), 577-590
DOI: 10.1002/prot.10363

All-Atom Structure Prediction and Folding Simulations of a Stable Protein
Simmerling, C., Strockbine, B and Roitberg, A.
Journal of American Chemical Society, 2002 , 124 (38), 11258-11259
DOI: 10.1021/ja0273851

Conformational Heterogeneity Observed in Simulations of a Pyrene-Substitued DNA
Cui, G and Simmerling, C.
Journal of American Chemical Society, 2002, 124 (41), 12154-12164
DOI: 10.1021/ja026825l

The Disordered Mobile Loop of GroES Folds into a Defined beta Hairpin upon Binding GroEL
Shewmaker, F., Maskos, K., Simmerling, C. and Landry, S. J.
Journal of Biological Chemistry , 2001 , 276 (33), 31257-31264
DOI: 10.1074/jbc.M102765200

Combining MONSSTER and LES/PME to Predict Protein Structure from Amino Acid Sequence: Application to the Small Protein CMTI-I
Simmerling, C., Lee, M.R, Ortiz, AR., Kolinski, A., Skolnick, J., Kollman, P.A.
Journal of American Chemical Society , 2000 , 122 (35), 8392-8402
DOI: 10.1021/ja993119k

Combined Locally Enhanced Sampling and Particle Mesh Ewald as a Strategy to Locate the Experimental Structure of a Non-helical Nucleic Acid
Simmerling, C., Miller, J. L., and Kollman, P.
Journal of American Chemical Society , 1998 , 120 (29), 7149-7155
DOI: 10.1021/ja9727023

The Use of Locally Enhanced Sampling in Free Energy Calculations: Testing and Application to the alpha -> beta Anomerization of Glucose
Simmerling, C., Fox, T. and Kollman, P.
Journal of American Chemical Society , 1998 , 120 (23), 5771-5782
DOI: 10.1021/ja972457n

AMBER 5
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.,
University of California, San Francisco, 1997

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

MOIL- A Program for Simulation of Macromolecules
Elber, R., Roitberg, A., Simmerling, C., Goldstein, R., Verkhivker, G., Li, H. and Ulitsky, A.
Computer Physics Communications, 1995 , 91 (1-3), 159-189
DOI: 10.1016/0010-4655(95)00047-J

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

Computer Determination of Peptide Conformations in Water: Different Roads to Structure
Simmerling, C. and Elber, R.
Proceedings of the National Academics of Sciences USA , 1995 , 92 (8), 3190-3193
PMCID: PMC42131

Hydrophobic “Collapse” in a Cyclic Hexapeptide: Computer Simulations of CHDLFC and CAAAAC in Water
Simmerling, C. and Elber, R.
Journal of American Chemical Society , 1994 , 16 (6), 2534-2547
DOI: 10.1021/ja00085a038

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

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