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Faculty


Carlos Simmerling

Carlos Simmerling, Professor

B.A., 1991, University of Illinois at Chicago
Ph.D., 1994, University of Illinois at Chicago
Postdoctoral Researcher, University of California, San Francisco, 1994-1998
2000 AMDeC Young Investigator Award

537  Chemistry / 119 Laufer Center
Phone: (631) 632-7950
Email: carlos.simmerling@stonybrook.edu

CLICK HERE FOR THE Simmerling GROUP WEB PAGE 

Computational Structural Biology

The goals of a computational chemist are to accurately simulate known properties of molecules, assist in the refinement and interpretation of experimental data and predict the results of future experiments. While quantum mechanical methods can be highly accurate, they are limited in that they currently cannot be applied to large systems such as proteins and nucleic acids, and little or no explicit solvent can be included in the calculations. Since the research in my lab involves relatively large biomolecular systems (such as proteins and nucleic acids) where specific interactions with solvent molecules are often important, we use the methods of molecular mechanics. Typical calculations involve molecular dynamics of the molecule of interest along with thousands of explicit solvent molecules, where the behavior of the molecule as a function of time is used to determine kinetic and thermodynamic properties of the system. These simulations can provide an atomic-detail picture of the behavior of a single molecule, rather than the time- and ensemble-averaged views that come from most experiments.

Research Interests

Program Development

One area of current research in my group is the development of new algorithms and programs for accurate and efficient simulation of large biomolecular systems using state-of-the-art computers. I am a member of the development teams for the widely used AMBER and MOIL suites of programs for molecular mechanics calculations. Among the many features of the programs are energy minimization, molecular dynamics, and calculation of free energies. Currently, we are improving the performance of the programs on massively parallel computers, developing efficient genetic algorithms that include solvent effects, evaluating a variety of methods for the inclusion of long-range electrostatic interactions and development of techniques to enhance conformational sampling during simulations of biologically relevant molecules.

Another area of interest in my lab is the development of tools for the visualization and analysis of the large amounts of data that are generated by our calculations. An example of this development is the program MOIL-View for visualization of the structure and dynamics of biomolecules.

Improved Simulation Methodologies: Conformational Sampling

The single largest roadblock to reliable calculations of structures and relative free energies for complex biomolecular systems is the sampling problem. The number of possible conformations for a flexible molecule increases exponentially with the number of rotatable bonds, rapidly exceeding the number which can realistically be evaluated. Overcoming the sampling limitation would have a tremendous impact on our ability to make significant contributions in many areas, such as docking of flexible ligands, refinement of structures with low resolution or incomplete data, quantitative calculation of effects of amino acid mutations on protein stability, assisting in the engineering of modified or new functions for enzymes and catalytic antibodies, and eventually, the "holy grail" of computational structural biology, the prediction of accurate three-dimensional protein structures from only sequence data. The methods that we develop and use must be compatible with the highest quality representations of the system, such as atomic detail, explicit solvation and accurate treatment of the long-range electrostatics that are critical in simulations of highly charged molecules such as DNA and RNA.

Structure Prediction

While the accurate prediction of structures from sequence data alone is a long-term goal, current projects involve the application of new sampling techniques to the study of systems where at least some data is available. Sources of this data include structures of homologous proteins, low-resolution or incomplete experimental data (such as that from X-ray crystallography or NMR spectroscopy), or low-resolution protein structure predictions from methods that forego atomic detail and explicit solvation.

Molecular Recognition

One current application involves prediction of the conformations of antibody hypervariable (antigen binding) loops. The overall structures of different antibodies are conserved despite their ability to recognize and bind diverse antigens, making them the ultimate biological mechanism for molecular recognition. We are developing methods that will predict these structures, including the locations and roles of key water molecules that often mediate antibody-ligand interactions. We also attempt to model and understand the conformational changes (induced fit) that often take place upon antigen binding, and assist in the development and optimization of catalytic antibodies.

Publications

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.,  Biochemistry201554 (30), 4683-4691
DOI: 10.1021/acs.biochem.5b00284

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 Computation201511 (8), 3696-3713
DOI: 10.1021/acs.jctc.5b00255

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 Computation201511 (8), 3714-3728
DOI: 10.1021/acs.jctc.5b00271

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 Research201543 (1), 272-281
DOI: 10.1093/nar/gku1300

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 Society2014136 (40), 13959-13962
DOI: 10.1021/ja503277669

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, 2014289, 17203-17214 
DOI: 10.1074/jbc.M114.571836

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 Biology20149, (4), 986–993 
DOI: 110.1021/cb400896g

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.,  ChemMedChem20149, (4), 776–791 
DOI: 10.1002/cmdc.201300429

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, J. Phys. Chem. Lett20145, 220-224 
DOI: 10.1021/jz4023738

Improved Generalized Born Solvent Model Parameters for Protein Simulations
Nguyen, H., Roe, D. R., Simmerling, C.,  Journal of Chemical Theory and Computation20139 (4), 2020-2034
DOI: 10.1021/ct3010485

Development of an Automated Event Detection Algorithm for HIV-1 Protease’s Flap Backbone Dihedral Change
Gee, J., Weaver, E., Shang, Y., Simmerling, C.,  J. Expt. Sec. Sci.20132(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 Chemistry2013288 , 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 Assignments20137(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,  J. Phys. Chem. B2012116, 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.,  J. Phys. Chem. B2012116, 10477-10489

Molecular dynamics applied in drug discovery: the case of HIV-1 protease
Shang, Y. and Simmerling, C.,  Computational Drug Discovery and Design2012, 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.,  Med. Chem. Letters20112, 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 Society2011133, 14504–14506 
DOI: 10.1021/ja205142d

An Overview of String-Based Path Sampling Methods
Bergonzo, C. and Simmerling, C.,  Annual Report in Computational Chemistry, 20117, 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.,  JJ. Mol. Graphics & Model.201129, 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 Journal201016, 12100-12103
DOI: 10.1002/chem.201002041

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 Computation20095 (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 Chemistry2009109, 3781-3790
DOI: 10.1002/qua.22405

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, 87-972010

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 Society2009131 (2), 430-431
DOI: 10.1021/ja807531v

Recent Advances in the Study of the Bioactive Conformation of Taxol
Sun, L., Simmerling, C. and Ojima, I.
ChemMedChem20094, 719-731
DOI: 10.1002/cmdc.200900044

Evaluating the Performance of the FF99SB Force Field Based on NMR Scalar Coupling Data
Wickstrom, L., Okur, A. and Simmerling, C.
Biophysical Journal200997 (3), 853-856
DOI: 10.1016/j.bpj.2009.04.063

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.
Biopolymers200889, 747-760
DOI: 10.1002/bip.21004

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 Society2008130 (23), 7184-7185
DOI: 10.1021/ja800893d

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 Computation20084 (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 Society2007129 (47), 14536-14537
DOI: 10.1021/ja075128w

Molecular Mechanics Parameters for the FapydG DNA lesion
Song, K., Hornak, V., de los Santos, C., Grollman, A. and Simmerling, C.
Journal of Computational Chemistry200729, 17-23
DOI: 10.1002/jcc.20625

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.
Biochemistry200746 (12), 3624-3634
DOI: 10.1021/bi061785+

Coupling of Replica Exchange Simulations to a non-Boltzmann structure reservoir
Roitberg, A., Okur, A. and Simmerling, C.
Journal of Physical Chemistry B2007111 (10), 2415-2418
DOI: 10.1021/jp068335b

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 B2007111 (7), 1846-1857
DOI: 10.1021/jp066831u

Targeting structural flexibility in HIV-1 protease inhibitor binding
Hornak, V. and Simmerling, C.
Drug Discovery Today200712 (3-4), 132-138
DOI: 10.1016/j.drudis.2006.12.011

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 Computation20073 (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 Computation20073 (1), 156-169
DOI: 10.1021/ct600085e

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, 2006103 (4), 915-920
DOI: 10.1073/pnas.0508452103

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 Society2006128 (9), 2812-2813
DOI: 10.1021/ja058211x

Simulating HIV-1 Protease at its Most Vulnerable Instant
Simmerling, C. and Gomperts, R.
Scientific Computing20067, 32-34

Enhanced Sampling Methods for Simulation of Nucleic Acids
Kelso, C. and Simmerling, C.
Computational Studies of DNA and RNA, Springer Publishers, 147-1862006

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 Amercian Chemical Society 2006128 (41), 13360-13361 
DOI: 10.1021/ja065133k 

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 

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 2006360 (5), 1094-1107 
DOI: 10.1016/j.jmb.2006.04.070 

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 Chemistry2006 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), 712-725 
DOI: 10.1002/prot.21123 

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 Computation2006 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 Computation2006 2 (2), 420-433 
DOI: 10.1021/ct050196z 

Enhanced Sampling Methods for Simulation of Nucleic Acids 
Kelso, C. and Simmerling, C. 
in 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 , 97-109 
DOI: 

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 & Biology 2005 12 (3), 339-348 
DOI: 10.1016/j.chembiol.2005.01.004 

Folding Cooperativity in a Three-stranded beta-sheet Model 
Roe, D., Hornak, V. and Simmerling, C. 
Journal of Molecular Biology2005352 (2), 370-381 
DOI: 10.1016/j.jmb.2005.07.036 

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 Society2005 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 Chemistry2005 26 , 1668- 
DOI: 

Modified Replica Exchange Simulation Methods for Local Structure Refinement 
Cheng, X., Cui, G., Hornak, V. and Simmerling, C. 
Journal of Physical Chemistry B2005109 (16), 8220-8230 
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 Chemistry2004 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 & 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 & Modeling200422 (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, Genetics2003 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 Society2002 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 Society2002124 (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 Francisco1997 

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.
Comp. Phys. Comm.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., 
in 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 
DOI: 

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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