Carlos Simmerling - Publications

Affiliations: 
Chemistry Stony Brook University, Stony Brook, NY, United States 

79 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Li H, Endutkin AV, Bergonzo C, Lin F, Grollman AP, Zharkov DO, Simmerling C. DNA deformation-coupled recognition of 8-oxoguanine: conformational kinetic gating in human DNA glycosylase. Journal of the American Chemical Society. PMID 28098999 DOI: 10.1021/jacs.6b11433  0.84
2016 Neckles CM, Pschibul A, Lai CE, Hirschbeck M, Kuper J, Davoodi S, Zou J, Liu N, Pan P, Shah S, Daryaee F, Bommineni GR, Lai C, Simmerling C, Kisker C, et al. Selectivity of Pyridone- and Diphenyl Ether-Based Inhibitors for the Yersinia pestis FabV Enoyl-ACP Reductase FabV. Biochemistry. PMID 27136302 DOI: 10.1021/acs.biochem.5b01301  1
2016 Perez A, Morrone JA, Simmerling C, Dill KA. Advances in free-energy-based simulations of protein folding and ligand binding. Current Opinion in Structural Biology. 36: 25-31. PMID 26773233 DOI: 10.1016/j.sbi.2015.12.002  1
2015 Hauser K, Essuman B, He Y, Coutsias E, Garcia-Diaz M, Simmerling C. A human transcription factor in search mode. Nucleic Acids Research. PMID 26673724 DOI: 10.1093/nar/gkv1091  1
2015 Nguyen H, Pérez A, Bermeo S, Simmerling C. Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins. Journal of Chemical Theory and Computation. 11: 3714-28. PMID 26574454 DOI: 10.1021/acs.jctc.5b00271  1
2015 Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. Journal of Chemical Theory and Computation. 11: 3696-713. PMID 26574453 DOI: 10.1021/acs.jctc.5b00255  1
2015 Perez A, MacCallum JL, Brini E, Simmerling C, Dill KA. Grid-Based Backbone Correction to the ff12SB Protein Force Field for Implicit-Solvent Simulations. Journal of Chemical Theory and Computation. 11: 4770-9. PMID 26574266 DOI: 10.1021/acs.jctc.5b00662  1
2015 Li H, Endutkin AV, Bergonzo C, Campbell AJ, de Los Santos C, Grollman A, Zharkov DO, Simmerling C. A dynamic checkpoint in oxidative lesion discrimination by formamidopyrimidine-DNA glycosylase. Nucleic Acids Research. PMID 26553802 DOI: 10.1093/nar/gkv1092  1
2015 Byrnes J, Hauser K, Norona L, Mejia E, Simmerling C, Garcia-Diaz M. Base Flipping by MTERF1 Can Accommodate Multiple Conformations and Occurs in a Stepwise Fashion. Journal of Molecular Biology. PMID 26523681 DOI: 10.1016/j.jmb.2015.10.021  1
2015 Lai CT, Li HJ, Yu W, Shah S, Bommineni GR, Perrone V, Garcia-Diaz M, Tonge PJ, Simmerling C. Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium tuberculosis InhA. Biochemistry. 54: 4683-91. PMID 26147157 DOI: 10.1021/acs.biochem.5b00284  0.64
2015 Kuznetsov NA, Bergonzo C, Campbell AJ, Li H, Mechetin GV, de los Santos C, Grollman AP, Fedorova OS, Zharkov DO, Simmerling C. Active destabilization of base pairs by a DNA glycosylase wedge initiates damage recognition. Nucleic Acids Research. 43: 272-81. PMID 25520195 DOI: 10.1093/nar/gku1300  1
2015 Lai CT, Li HJ, Yu W, Shah S, Bommineni GR, Perrone V, Garcia-Diaz M, Tonge PJ, Simmerling C. Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium tuberculosis InhA Biochemistry. 54: 4683-4691. DOI: 10.1021/acs.biochem.5b00284  1
2014 Nguyen H, Maier J, Huang H, Perrone V, Simmerling C. Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent. Journal of the American Chemical Society. 136: 13959-62. PMID 25255057 DOI: 10.1021/ja5032776  1
2014 Huang X, Britto MD, Kear-Scott JL, Boone CD, Rocca JR, Simmerling C, Mckenna R, Bieri M, Gooley PR, Dunn BM, Fanucci GE. The role of select subtype polymorphisms on HIV-1 protease conformational sampling and dynamics. The Journal of Biological Chemistry. 289: 17203-14. PMID 24742668 DOI: 10.1074/jbc.M114.571836  1
2014 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, et al. Ultrafast Structural Dynamics of BlsA, a Photoreceptor from the Pathogenic Bacterium Acinetobacter baumannii. The Journal of Physical Chemistry Letters. 5: 220-224. PMID 24723998 DOI: 10.1021/jz4023738  1
2014 Li HJ, Lai CT, Pan P, Yu W, Liu N, Bommineni GR, Garcia-Diaz M, Simmerling C, Tonge PJ. A structural and energetic model for the slow-onset inhibition of the Mycobacterium tuberculosis enoyl-ACP reductase InhA. Acs Chemical Biology. 9: 986-93. PMID 24527857 DOI: 10.1021/cb400896g  1
2013 Nguyen H, Roe DR, Simmerling C. Improved Generalized Born Solvent Model Parameters for Protein Simulations. Journal of Chemical Theory and Computation. 9: 2020-2034. PMID 25788871 DOI: 10.1021/ct3010485  1
2013 Kapilashrami K, Bommineni GR, Machutta CA, Kim P, Lai CT, Simmerling C, Picart F, Tonge PJ. Thiolactomycin-based β-ketoacyl-AcpM synthase A (KasA) inhibitors: fragment-based inhibitor discovery using transient one-dimensional nuclear overhauser effect NMR spectroscopy. The Journal of Biological Chemistry. 288: 6045-52. PMID 23306195 DOI: 10.1074/jbc.M112.414516  1
2013 Huang X, de Vera IM, Veloro AM, Rocca JR, Simmerling C, Dunn BM, Fanucci GE. Backbone ¹H, ¹³C, and ¹⁵N chemical shift assignment for HIV-1 protease subtypes and multi-drug resistant variant MDR 769. Biomolecular Nmr Assignments. 7: 199-202. PMID 22752791 DOI: 10.1007/s12104-012-9409-7  1
2012 Huang X, de Vera IM, Veloro AM, Blackburn ME, Kear JL, Carter JD, Rocca JR, Simmerling C, Dunn BM, Fanucci GE. Inhibitor-induced conformational shifts and ligand-exchange dynamics for HIV-1 protease measured by pulsed EPR and NMR spectroscopy. The Journal of Physical Chemistry. B. 116: 14235-44. PMID 23167829 DOI: 10.1021/jp308207h  1
2012 Eilers M, Goncalves JA, Ahuja S, Kirkup C, Hirshfeld A, Simmerling C, Reeves PJ, Sheves M, Smith SO. Structural transitions of transmembrane helix 6 in the formation of metarhodopsin I. The Journal of Physical Chemistry. B. 116: 10477-89. PMID 22564141 DOI: 10.1021/jp3019183  1
2012 Shang Y, Simmerling C. Molecular dynamics applied in drug discovery: the case of HIV-1 protease. Methods in Molecular Biology (Clifton, N.J.). 819: 527-49. PMID 22183556 DOI: 10.1007/978-1-61779-465-0_31  1
2011 Li X, Liu N, Zhang H, Knudson SE, Li HJ, Lai CT, Simmerling C, Slayden RA, Tonge PJ. CoA Adducts of 4-Oxo-4-Phenylbut-2-enoates: Inhibitors of MenB from the M. tuberculosis Menaquinone Biosynthesis Pathway. Acs Medicinal Chemistry Letters. 2: 818-823. PMID 22267981 DOI: 10.1021/ml200141e  1
2011 Bergonzo C, Campbell AJ, de los Santos C, Grollman AP, Simmerling C. Energetic preference of 8-oxoG eversion pathways in a DNA glycosylase. Journal of the American Chemical Society. 133: 14504-6. PMID 21848286 DOI: 10.1021/ja205142d  1
2011 Shang Y, Nguyen H, Wickstrom L, Okur A, Simmerling C. Improving the description of salt bridge strength and geometry in a Generalized Born model. Journal of Molecular Graphics & Modelling. 29: 676-84. PMID 21168352 DOI: 10.1016/j.jmgm.2010.11.013  1
2011 Altun A, Bartlett RJ, Bergonzo C, Braun AR, Bylaska EJ, Daniel Crawford T, de Jong WA, Deumens E, Erik Nielsen J, Fortenberry RC, Govind N, Hayat S, Helms V, Jindal N, Johnston MA, ... ... Simmerling C, et al. Contributors Annual Reports in Computational Chemistry. 7: ix-xi. DOI: 10.1016/B978-0-444-53835-2.00017-1  1
2011 Bergonzo C, Simmerling C. An Overview of String-Based Path Sampling Methods Annual Reports in Computational Chemistry. 7: 89-97. DOI: 10.1016/B978-0-444-53835-2.00004-3  1
2010 Guainazzi A, Campbell AJ, Angelov T, Simmerling C, Schärer OD. Synthesis and molecular modeling of a nitrogen mustard DNA interstrand crosslink. Chemistry (Weinheim An Der Bergstrasse, Germany). 16: 12100-3. PMID 20842675 DOI: 10.1002/chem.201002041  1
2010 Luchko T, Gusarov S, Roe DR, Simmerling C, Case DA, Tuszynski J, Kovalenko A. Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber. Journal of Chemical Theory and Computation. 6: 607-624. PMID 20440377 DOI: 10.1021/ct900460m  1
2010 Machutta CA, Bommineni GR, Luckner SR, Kapilashrami K, Ruzsicska B, Simmerling C, Kisker C, Tonge PJ. Slow onset inhibition of bacterial beta-ketoacyl-acyl carrier protein synthases by thiolactomycin. The Journal of Biological Chemistry. 285: 6161-9. PMID 20018879 DOI: 10.1074/jbc.M109.077909  1
2009 Song K, Campbell AJ, Bergonzo C, de Los Santos C, Grollman AP, Simmerling C. An Improved Reaction Coordinate for Nucleic Acid Base Flipping Studies. Journal of Chemical Theory and Computation. 5: 3105-13. PMID 26609990 DOI: 10.1021/ct9001575  1
2009 Bergonzo C, Campbell AJ, Walker RC, Simmerling C. A Partial Nudged Elastic Band Implementation for Use with Large or Explicitly Solvated Systems. International Journal of Quantum Chemistry. 109: 3781. PMID 20148191 DOI: 10.1002/qua.22405  1
2009 Wickstrom L, Okur A, Simmerling C. Evaluating the performance of the ff99SB force field based on NMR scalar coupling data. Biophysical Journal. 97: 853-6. PMID 19651043 DOI: 10.1016/j.bpj.2009.04.063  1
2009 Sun L, Simmerling C, Ojima I. Recent advances in the study of the bioactive conformation of taxol. Chemmedchem. 4: 719-31. PMID 19360801 DOI: 10.1002/cmdc.200900044  1
2009 Galiano L, Ding F, Veloro AM, Blackburn ME, Simmerling C, Fanucci GE. Drug pressure selected mutations in HIV-1 protease alter flap conformations Journal of the American Chemical Society. 131: 430-431. DOI: 10.1021/ja807531v  1
2008 Okur A, Wickstrom L, Simmerling C. Evaluation of Salt Bridge Structure and Energetics in Peptides Using Explicit, Implicit, and Hybrid Solvation Models. Journal of Chemical Theory and Computation. 4: 488-98. PMID 26620789 DOI: 10.1021/ct7002308  1
2008 Sun L, Geng X, Geney R, Li Y, Simmerling C, Li Z, Lauher JW, Xia S, Horwitz SB, Veith JM, Pera P, Bernacki RJ, Ojima I. Design, synthesis, and biological evaluation of novel C14-C3'BzN-linked macrocyclic taxoids. The Journal of Organic Chemistry. 73: 9584-93. PMID 18975909 DOI: 10.1021/jo801713q  1
2008 Ding F, Layten M, Simmerling C. Solution structure of HIV-1 protease flaps probed by comparison of molecular dynamics simulation ensembles and EPR experiments. Journal of the American Chemical Society. 130: 7184-5. PMID 18479129 DOI: 10.1021/ja800893d  1
2008 Song K, Stewart JM, Fesinmeyer RM, Andersen NH, Simmerling C. Structural insights for designed alanine-rich helices: comparing NMR helicity measures and conformational ensembles from molecular dynamics simulation. Biopolymers. 89: 747-60. PMID 18428207 DOI: 10.1002/bip.21004  1
2008 Song K, Hornak V, de los Santos C, Grollman AP, Simmerling C. Molecular mechanics parameters for the FapydG DNA lesion. Journal of Computational Chemistry. 29: 17-23. PMID 17551974 DOI: 10.1002/jcc.20625  1
2007 Okur A, Roe DR, Cui G, Hornak V, Simmerling C. Improving Convergence of Replica-Exchange Simulations through Coupling to a High-Temperature Structure Reservoir. Journal of Chemical Theory and Computation. 3: 557-68. PMID 26637035 DOI: 10.1021/ct600263e  1
2007 Song K, Kelso C, de los Santos C, Grollman AP, Simmerling C. Molecular simulations reveal a common binding mode for glycosylase binding of oxidatively damaged DNA lesions. Journal of the American Chemical Society. 129: 14536-7. PMID 17988127 DOI: 10.1021/ja075128w  1
2007 Wickstrom L, Bi Y, Hornak V, Raleigh DP, Simmerling C. 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. Biochemistry. 46: 3624-34. PMID 17338549 DOI: 10.1021/bi061785+  1
2007 Roitberg AE, Okur A, Simmerling C. Coupling of replica exchange simulations to a non-Boltzmann structure reservoir. The Journal of Physical Chemistry. B. 111: 2415-8. PMID 17300191 DOI: 10.1021/jp068335b  1
2007 Hornak V, Simmerling C. Targeting structural flexibility in HIV-1 protease inhibitor binding. Drug Discovery Today. 12: 132-8. PMID 17275733 DOI: 10.1016/j.drudis.2006.12.011  1
2007 Roe DR, Okur A, Wickstrom L, Hornak V, Simmerling C. Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation. The Journal of Physical Chemistry. B. 111: 1846-57. PMID 17256983 DOI: 10.1021/jp066831u  1
2006 Okur A, Wickstrom L, Layten M, Geney R, Song K, Hornak V, Simmerling C. Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model. Journal of Chemical Theory and Computation. 2: 420-33. PMID 26626529 DOI: 10.1021/ct050196z  1
2006 Geney R, Layten M, Gomperts R, Hornak V, Simmerling C. Investigation of Salt Bridge Stability in a Generalized Born Solvent Model. Journal of Chemical Theory and Computation. 2: 115-27. PMID 26626386 DOI: 10.1021/ct050183l  1
2006 Layten M, Hornak V, Simmerling C. The open structure of a multi-drug-resistant HIV-1 protease is stabilized by crystal packing contacts. Journal of the American Chemical Society. 128: 13360-1. PMID 17031940 DOI: 10.1021/ja065133k  1
2006 Rafi S, Novichenok P, Kolappan S, Zhang X, Stratton CF, Rawat R, Kisker C, Simmerling C, Tonge PJ. Structure of acyl carrier protein bound to FabI, the FASII enoyl reductase from Escherichia coli. The Journal of Biological Chemistry. 281: 39285-93. PMID 17012233 DOI: 10.1074/jbc.M608758200  1
2006 Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins. 65: 712-25. PMID 16981200 DOI: 10.1002/prot.21123  1
2006 Song K, Hornak V, de Los Santos C, Grollman AP, Simmerling C. Computational analysis of the mode of binding of 8-oxoguanine to formamidopyrimidine-DNA glycosylase. Biochemistry. 45: 10886-94. PMID 16953574 DOI: 10.1021/bi060380m  1
2006 Rafi SB, Cui G, Song K, Cheng X, Tonge PJ, Simmerling C. Insight through molecular mechanics Poisson-Boltzmann surface area calculations into the binding affinity of triclosan and three analogues for FabI, the E. coli enoyl reductase. Journal of Medicinal Chemistry. 49: 4574-80. PMID 16854062 DOI: 10.1021/jm060222t  1
2006 Wickstrom L, Okur A, Song K, Hornak V, Raleigh DP, Simmerling CL. The unfolded state of the villin headpiece helical subdomain: computational studies of the role of locally stabilized structure. Journal of Molecular Biology. 360: 1094-107. PMID 16797585 DOI: 10.1016/j.jmb.2006.04.070  1
2006 Hornak V, Okur A, Rizzo RC, Simmerling C. HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state. Journal of the American Chemical Society. 128: 2812-3. PMID 16506755 DOI: 10.1021/ja058211x  1
2006 Hornak V, Okur A, Rizzo RC, Simmerling C. HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. 103: 915-20. PMID 16418268 DOI: 10.1073/pnas.0508452103  1
2006 Okur A, Simmerling C. Chapter 6 Hybrid Explicit/Implicit Solvation Methods Annual Reports in Computational Chemistry. 2: 97-109. DOI: 10.1016/S1574-1400(06)02006-8  1
2006 Kelso C, Simmerling C. Enhanced sampling methods for atomistic simulation of nucleic acids Computational Studies of Rna and Dna. 147-167. DOI: 10.1007/978-1-4020-4851-3_6  1
2006 Simmerling C, Gomperts R. Simulating hiv-1 protease at its most vulnerable instant Scientific Computing. 23: 32-34.  1
2005 Cheng X, Cui G, Hornak V, Simmerling C. Modified replica exchange simulation methods for local structure refinement. The Journal of Physical Chemistry. B. 109: 8220-30. PMID 16851961 DOI: 10.1021/jp045437y  1
2005 Cheng X, Kelso C, Hornak V, de los Santos C, Grollman AP, Simmerling C. Dynamic behavior of DNA base pairs containing 8-oxoguanine. Journal of the American Chemical Society. 127: 13906-18. PMID 16201812 DOI: 10.1021/ja052542s  1
2005 Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ. The Amber biomolecular simulation programs. Journal of Computational Chemistry. 26: 1668-88. PMID 16200636 DOI: 10.1002/jcc.20290  1
2005 Roe DR, Hornak V, Simmerling C. Folding cooperativity in a three-stranded beta-sheet model. Journal of Molecular Biology. 352: 370-81. PMID 16095612 DOI: 10.1016/j.jmb.2005.07.036  1
2005 Geney R, Sun L, Pera P, Bernacki RJ, Xia S, Horwitz SB, Simmerling CL, Ojima I. Use of the tubulin bound paclitaxel conformation for structure-based rational drug design. Chemistry & Biology. 12: 339-48. PMID 15797218 DOI: 10.1016/j.chembiol.2005.01.004  1
2005 Kubatzky KF, Liu W, Goldgraben K, Simmerling C, Smith SO, Constantinescu SN. Structural requirements of the extracellular to transmembrane domain junction for erythropoietin receptor function. The Journal of Biological Chemistry. 280: 14844-54. PMID 15657048 DOI: 10.1074/jbc.M411251200  1
2004 Hornak V, Simmerling C. Development of softcore potential functions for overcoming steric barriers in molecular dynamics simulations. Journal of Molecular Graphics & Modelling. 22: 405-13. PMID 15099836 DOI: 10.1016/j.jmgm.2003.12.007  1
2004 Sivaraman S, Sullivan TJ, Johnson F, Novichenok P, Cui G, Simmerling C, Tonge PJ. Inhibition of the bacterial enoyl reductase FabI by triclosan: a structure-reactivity analysis of FabI inhibition by triclosan analogues. Journal of Medicinal Chemistry. 47: 509-18. PMID 14736233 DOI: 10.1021/jm030182i  1
2004 Roitberg A, Simmerling C. Journal of Molecular Graphics and Modelling: Foreword Journal of Molecular Graphics and Modelling. 22: 317. DOI: 10.1016/j.jmgm.2004.03.015  1
2004 Cheng X, Hornak V, Simmerling C. Improved conformational sampling through an efficient combination of mean-field simulation approaches Journal of Physical Chemistry B. 108: 426-437.  1
2003 Hornak V, Simmerling C. Generation of accurate protein loop conformations through low-barrier molecular dynamics. Proteins. 51: 577-90. PMID 12784217 DOI: 10.1002/prot.10363  1
2003 Okur A, Strockbine B, Hornak V, Simmerling C. Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins. Journal of Computational Chemistry. 24: 21-31. PMID 12483672 DOI: 10.1002/jcc.10184  1
2002 Cui G, Simmerling C. Conformational heterogeneity observed in simulations of a pyrene-substituted DNA. Journal of the American Chemical Society. 124: 12154-64. PMID 12371855 DOI: 10.1021/ja026825l  1
2002 Simmerling C, Strockbine B, Roitberg AE. All-atom structure prediction and folding simulations of a stable protein. Journal of the American Chemical Society. 124: 11258-9. PMID 12236726 DOI: 10.1021/ja0273851  1
2001 Shewmaker F, Maskos K, Simmerling C, Landry SJ. The disordered mobile loop of GroES folds into a defined beta-hairpin upon binding GroEL. The Journal of Biological Chemistry. 276: 31257-64. PMID 11395498 DOI: 10.1074/jbc.M102765200  1
2000 Simmerling C, Lee MR, Ortiz AR, Kolinski A, Skolnick J, Kollman PA. Combining MONSSTER and LES/PME to predict protein structure from amino acid sequence: Application to the small protein CMTI-1 Journal of the American Chemical Society. 122: 8392-8402.  1
1998 Simmerling C, Miller JL, Kollman PA. Combined locally enhanced sampling and Particle Mesh Ewald as a strategy to locate the experimental structure of a nonhelical nucleic acid Journal of the American Chemical Society. 120: 7149-7155. DOI: 10.1021/ja9727023  1
1998 Simmerling C, Fox T, Kollman PA. Use of locally enhanced sampling in free energy calculations: Testing and application to the α → β anomerization of glucose Journal of the American Chemical Society. 120: 5771-5782. DOI: 10.1021/ja972457n  1
1995 Simmerling CL, Elber R. Computer determination of peptide conformations in water: different roads to structure. Proceedings of the National Academy of Sciences of the United States of America. 92: 3190-3. PMID 7724538  1
1995 Elber R, Roitberg A, Simmerling C, Goldstein R, Li H, Verkhivker G, Keasar C, Zhang J, Ulitsky A. MOIL: A program for simulations of macromolecules Computer Physics Communications. 91: 159-189. DOI: 10.1016/0010-4655(95)00047-J  1
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