SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein Stepanenko, Darya; Budhan, Stephanie; Simmerling, Carlos, J. Chem. Inf. Model., 2023, 63, 4, 1087–1092. DOI:10.1021/acs.jcim.2c01366

SARS-CoV-2 spike conformation determines plasma neutralizing activity elicited by a wide panel of human vaccines. John E. Bowen, Young-Jun Park, Cameron Stewart, Jack T. Brown, William K. Sharkey, Alexandra C. Walls, Anshu Joshi, Kaitlin R. Sprouse, Matthew Mccallum, M. Alejandra Tortorici, Nicholas M. Franko, Jennifer K. Logue, Ignacio G. Mazzitelli, Annalee W. Nguyen, Rui P. Silva, Yimin Huang, Jun Siong Low, Josipa Jerak, Sasha W Tiles, Kumail Ahmed, Asefa Shariq, Jennifer M. Dan, Zeli Zhang, Daniela Weiskopf, Alessandro Sette, Gyorgy Snell, Christine M. Posavad, Najeeha Talat Iqbal, Jorge Geffner, Alessandra Bandera, Andrea Gori, Federica Sallusto, Jennifer A. Maynard, Shane Crotty, Wesley C. Van Voorhis, Carlos Simmerling, Renata Grifantini, Helen Y. Chu, Davide Corti, and David Veesler, Science Immunology, 2022, DOI: 10.1126/sciimmunol.adf1421

BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions Mina Nikolić, Sandi Brudar, Evangelos Coutsias, Ken A. Dill, Miha Lukšič, Carlos Simmerling and Barbara Hribar-Lee, Int. J. Molecular Sciences, 2022, 23(23), 15371; DOI: 10.3390/ijms232315371

On the Plasticity of Amyloid Formation: The Impact of Destabilizing Small to Large Substitutions on IAPP Amyloid Formation. Lakshan Manathunga, Rehena Akter, Alexander Zhyvoloup, Carlos Simmerling and Daniel Raleigh; Protein Science, in press 2022, DOI: 10.1002/pro.4539

Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir. Kenneth Lam, Koushik Kasavajhala, Sarah Gunasekera, and Carlos Simmerling, J. Chem. Theory Comput. 2022, 18, 6, 3930–3947

GlycoGrip: Cell Surface-Inspired Universal Sensor for Betacoronaviruses. Sang Hoon Kim, Fiona L. Kearns, Mia A. Rosenfeld, Lorenzo Casalino, Micah J. Papanikolas, Carlos Simmerling, Rommie E. Amaro, and Ronit Freeman, ACS Cent. Sci. 2021. doi.org/10.1021/acscentsci.1c01080

Receptor binding may directly activate the fusion machinery in coronavirus spike glycoproteins. Yuzhang Wang, Lucy Fallon, Lauren Raguette, Stephanie Budhan, Kellon Belfon, Darya Stepanenko, Stephanie Helbock, Sarah Varghese, Carlos Simmerling, preprint

Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies. Junjie Zou, Zhipeng Li, Shuai Liu, Chunwang Peng, Dong Fang, Xiao Wan, Zhixiong Lin, Tai-Sung Lee, Daniel P. Raleigh, Mingjun Yang, and Carlos Simmerling*, J. Chem. Theory & Comput., J. Chem. Theory Comput. 2021, 17, 6, 3710–3726.

Quantitative Analysis of Protein Unfolded State Energetics: Experimental and Computational Studies Demonstrate That Non-Native Side-Chain Interactions Stabilize Local Native Backbone Structure. Junjie Zou, Shifeng Xiao, Carlos Simmerling, Daniel Raleigh, J. Phys. Chem. B, 2021, 125, 13, 3269–3277

AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics. Lorenzo Casalino, Abigail Dommer, Zied Gaieb, Emilia P. Barros, Terra Sztain, Surl-Hee Ahn, Anda Trifan, Alexander Brace, Anthony Bogetti, Heng Ma, Hyungro Lee, Matteo Turilli, Syma Khalid, Lillian Chong, Carlos Simmerling, David J. Hardy, Julio D. C. Maia, James C. Phillips, Thorsten Kurth, Abraham Stern, Lei Huang, John McCalpin, Mahidhar Tatineni, Tom Gibbs, John E. Stone, Shantenu Jha, Arvind Ramanathan, Rommie E. Amaro, International Journal of High Performance Computing Applications, 35, 5, 2021, 432-451. doi.org/10.1177/10943420211006452

Free Energy Landscapes from SARS-CoV-2 Spike Glycoprotein Simulations Suggest that RBD Opening Can Be Modulated via Interactions in an Allosteric Pocket. Lucy Fallon, Kellon A. A. Belfon, Lauren Raguette, Yuzhang Wang, Darya Stepanenko, Abbigayle Cuomo, Jose Guerra, Stephanie Budhan, Sarah Varghese, Christopher P. Corbo, Robert C. Rizzo, and Carlos Simmerling, J. Am. Chem. Soc., 2021, 143, 30, 11349–11360. doi.org/10.1021/jacs.1c00556 PMCID:8315243

The flexibility of ACE2 in the context of SARS-CoV-2 infection. E. P. Barros, L. Casalino, Z. Gaieb, A. C. Dommer, Y. Wang, L. Fallon, L. Raguette, K. Belfon, C. Simmerling, R. E. Amaro, Biophysical Journal Special Issue on COVID-19, Volume 120, Issue 6, 16 March 2021, 1072-1084. doi.org/10.1016/j.bpj.2020.10.036

Protein storytelling through physics E. Brini, C. Simmerling, K. Dill, Science, Nov. 2020

Exploring Protocols to Build Reservoirs to Accelerate Temperature Replica Exchange MD Simulations. Kasavajhala, Koushik; Lam, Kenneth; Simmerling, Carlos. Journal of Chemical Theory & Computation, J. Chem. Theory Comput. 2020, 16, 12, 7776–7799

Unraveling the Mechanism of a LOV Domain Optogenetic Sensor: A Glutamine Lever Induces Unfolding of the Jα Helix . James N. Iuliano, Jinnette Tolentino Collado, Agnieszka A. Gil, Pavithran T. Ravindran, Andras Lukacs, SeungYoun Shin, Helena A. Woroniecka, Katrin Adamczyk, James M. Aramini, Uthama R. Edupuganti, Christopher R. Hall, Gregory M. Greetham, Igor V. Sazanovich, Ian P. Clark, Taraneh Daryaee, Jared E. Toettcher, Jarrod B. French, Kevin H. Gardner, Carlos L. Simmerling, Stephen R. Meech, and Peter J. Tonge. ACS Chem. Biol. 2020, 15, 10, 2752–2765

Copper stabilizes antiparallel β-sheet fibrils of the amyloid β40 (Aβ40)-Iowa variant. Elliot J. Crooks, Brandon A. Irizarry, Martine Ziliox, Toru Kawakami, Tiffany Victor, Feng Xu, Hironobu Hojo, Kelley Chiu, Carlos Simmerling, William E. Van Nostrand, Steven O. Smith and Lisa M. Miller, The Journal of Biological Chemistry 295, 2020.

ff19SB: Amino-Acid Specific Protein Backbone Parameters Trained Against Quantum Mechanics Energy Surfaces in Solution. Tian, C., Kasavajhala, K., Belfon, K., Raguette, L., Huang, H., Migues, A., Bickel, J., Wang, Y., Pincay, J., Wu, Q., Simmerling, C., The Journal of Chemical Theory and Computation 16 (1), 2019

A Fast Implementation of the Nudged Elastic Band Method in AMBER. Ghoreishi, D., Cerutti, D., Fallon, Z., Simmerling, C., Roitberg, A., The Journal of Chemical Theory and Computation 2019, 15, 4699−4707.

Blinded Prediction of Protein-Ligand Binding Affinity Using Amber Thermodynamic Integration for the 2018 D3R Grand Challenge 4. Zou, J., Tian, C., Simmerling, C., J Comput Aided Mol Des 33, 1021–1029 (2019).

Dissecting the Energetics of Intrinsically Disordered Proteins via a Hybrid Experimental and Computational Approach. Zou, J., Simmerling, C., Raleigh, D., The Journal of Physical Chemistry B 123 (49), 10394-10402 2019

Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs. Huang, H. and Simmerling, C., Journal of Chemical Theory and Computation, 2018,

Laguerre-Intersection Method for Implicit Solvation. Hummel, M. H., Yu, B., Simmerling, C., Coutsias, E., Int J Comput Geom Appl. 2018 Mar; 28(1): 1–38.

Characterization of Biomolecular Helices and Their Complementarity Using Geometric Analysis. Hauser, K., Yiqing, H., Garcia-Diaz, M., Simmerling, C., Coustais, E., Journal of Chemical Information and Modeling, 2017.

DNA Deformation-Coupled Recognition of 8‑Oxoguanine: Conformational Kinetic Gating in Human DNA Glycosylase. Li, H., Endutkin, A., Bergonzo, C., Fu, L., Grollman, A., Zharkov, D., Simmerling, C., Journal of the American Chemical Society, 2017, 139 (7), 2682-2692

Experimental and Computational Analysis of Protein Stabilization by Gly-to-D-Ala Substitution: A Convolution of Native State and Unfolded State Effects. Zou, J., Song, B., Simmerling, C., Raleigh, D., Journal of the American Chemical Society, 2016, 138 (48), 15682–15689

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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. Journal of the American Chemical Society, 2009, 131 (2), 430-431

Recent Advances in the Study of the Bioactive Conformation of Taxol. Sun, L., Simmerling, C. and Ojima, I. ChemMedChem, 2009, 4, 719-731

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

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

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

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

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

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

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

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

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

Targeting structural flexibility in HIV-1 protease inhibitor binding. Hornak, V. and Simmerling, C. Drug Discovery Today, 2007, 12 (3-4), 132-138

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

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

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

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

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

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

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

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

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

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

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

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

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 Methods02006-8). 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

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

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

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

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 , 1668-88.

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

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

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

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

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

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

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

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

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

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

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

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

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

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 Macromolecules00047-J). Elber, R., Roitberg, A., Simmerling, C., Goldstein, R., Verkhivker, G., Li, H. and Ulitsky, A. Computer Physics Communications, 1995 , 91 (1-3), 159-189

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

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

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