| Year |
Citation |
Score |
| 2024 |
Cao X, Hummel MH, Wang Y, Simmerling C, Coutsias EA. Exact analytical algorithm for solvent accessible surface area and derivatives in implicit solvent molecular simulations on GPUs. Arxiv. PMID 38313200 |
0.686 |
|
| 2023 |
Case DA, Aktulga HM, Belfon K, Cerutti DS, Cisneros GA, Cruzeiro VWD, Forouzesh N, Giese TJ, Götz AW, Gohlke H, Izadi S, Kasavajhala K, Kaymak MC, King E, Kurtzman T, ... ... Simmerling C, et al. AmberTools. Journal of Chemical Information and Modeling. 63: 6183-6191. PMID 37805934 DOI: 10.1021/acs.jcim.3c01153 |
0.68 |
|
| 2023 |
Kasavajhala K, Simmerling C. Exploring the Transferability of Replica Exchange Structure Reservoirs to Accelerate Generation of Ensembles for Alternate Hamiltonians or Protein Mutations. Journal of Chemical Theory and Computation. 19: 1931-1944. PMID 36861842 DOI: 10.1021/acs.jctc.3c00005 |
0.346 |
|
| 2022 |
Nikolić M, Brudar S, Coutsias E, Dill KA, Lukšič M, Simmerling C, Hribar-Lee B. BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions. International Journal of Molecular Sciences. 23. PMID 36499696 DOI: 10.3390/ijms232315371 |
0.616 |
|
| 2021 |
Zou J, Li Z, Liu S, Peng C, Fang D, Wan X, Lin Z, Lee TS, Raleigh DP, Yang M, Simmerling C. Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies. Journal of Chemical Theory and Computation. PMID 34029468 DOI: 10.1021/acs.jctc.1c00214 |
0.307 |
|
| 2019 |
Tian C, Kasavajhala K, Belfon KAA, Raguette L, Huang H, Migues AN, Bickel J, Wang Y, Pincay J, Wu Q, Simmerling C. ff19SB: Amino-acid specific protein backbone parameters trained against quantum mechanics energy surfaces in solution. Journal of Chemical Theory and Computation. PMID 31714766 DOI: 10.1021/Acs.Jctc.9B00591 |
0.437 |
|
| 2019 |
Zou J, Simmerling C, Raleigh DP. Dissecting the Energetics of Intrinsically Disordered Proteins via a Hybrid Experimental and Computational Approach. The Journal of Physical Chemistry. B. PMID 31702919 DOI: 10.1021/Acs.Jpcb.9B08323 |
0.392 |
|
| 2019 |
Zou J, Tian C, Simmerling C. Blinded prediction of protein-ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4. Journal of Computer-Aided Molecular Design. PMID 31555923 DOI: 10.1007/S10822-019-00223-X |
0.347 |
|
| 2019 |
Ghoreishi D, Cerutti DS, Fallon Z, Simmerling C, Roitberg AE. A Fast Implementation of the Nudged Elastic Band Method in AMBER. Journal of Chemical Theory and Computation. PMID 31314523 DOI: 10.1021/Acs.Jctc.9B00329 |
0.372 |
|
| 2018 |
Hummel MH, Yu B, Simmerling C, Coutsias EA. LAGUERRE-INTERSECTION METHOD FOR IMPLICIT SOLVATION. International Journal of Computational Geometry & Applications. 28: 1-38. PMID 30853740 DOI: 10.1142/S0218195918500012 |
0.7 |
|
| 2018 |
Huang H, Simmerling C. A Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs. Journal of Chemical Theory and Computation. PMID 30303377 DOI: 10.1021/Acs.Jctc.8B00413 |
0.451 |
|
| 2017 |
Hauser K, He Y, Garcia-Diaz M, Simmerling C, Coutsias EA. Characterization of Biomolecular Helices and Their Complementarity Using Geometric Analysis. Journal of Chemical Information and Modeling. PMID 28287728 DOI: 10.1021/Acs.Jcim.6B00721 |
0.686 |
|
| 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 |
0.73 |
|
| 2016 |
Zou J, Song B, Simmerling C, Raleigh D. Experimental and Computational Analysis of Protein Stabilization by Gly-to-d-Ala Substitution: A Convolution of Native State and Unfolded State Effects. Journal of the American Chemical Society. 138: 15682-15689. PMID 27934019 DOI: 10.1021/Jacs.6B09511 |
0.389 |
|
| 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 |
0.46 |
|
| 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 |
0.675 |
|
| 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 |
0.415 |
|
| 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 |
0.795 |
|
| 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 |
0.428 |
|
| 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 |
0.776 |
|
| 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 |
0.376 |
|
| 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 |
0.363 |
|
| 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 |
0.773 |
|
| 2015 |
Nguyen H, Maier J, Huang H, Perrone V, Perez A, Simmerling C. Simulating Protein and Nucleic Acid Dynamics on the Microsecond to Millisecond Timescale Biophysical Journal. 108: 49a. DOI: 10.1016/J.Bpj.2014.11.302 |
0.485 |
|
| 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 |
0.498 |
|
| 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 |
0.399 |
|
| 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 |
0.764 |
|
| 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 |
0.324 |
|
| 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 |
0.318 |
|
| 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 |
0.6 |
|
| 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 |
0.773 |
|
| 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 |
0.815 |
|
| 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 |
0.613 |
|
| 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 |
0.7 |
|
| 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 |
0.637 |
|
| 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 |
0.74 |
|
| 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 |
0.784 |
|
| 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 |
0.774 |
|
| 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 |
0.786 |
|
| 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 |
0.371 |
|
| 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: 430-1. PMID 19140783 DOI: 10.1021/Ja807531V |
0.355 |
|
| 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 |
0.802 |
|
| 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 |
0.312 |
|
| 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 |
0.306 |
|
| 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 |
0.422 |
|
| 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 |
0.484 |
|
| 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 |
0.807 |
|
| 2007 |
Mongan J, Simmerling C, McCammon JA, Case DA, Onufriev A. Generalized Born model with a simple, robust molecular volume correction. Journal of Chemical Theory and Computation. 3: 156-169. PMID 21072141 DOI: 10.1021/ct600085e |
0.303 |
|
| 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 |
0.326 |
|
| 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+ |
0.732 |
|
| 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 |
0.636 |
|
| 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 |
0.366 |
|
| 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 |
0.802 |
|
| 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 |
0.8 |
|
| 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 |
0.398 |
|
| 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 |
0.322 |
|
| 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 |
0.384 |
|
| 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 |
0.788 |
|
| 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 |
0.419 |
|
| 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 |
0.63 |
|
| 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 |
0.788 |
|
| 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 |
0.619 |
|
| 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 |
0.633 |
|
| 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 |
0.64 |
|
| 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 |
0.714 |
|
| 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 |
0.575 |
|
| 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 |
0.331 |
|
| 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 |
0.742 |
|
| 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 |
0.305 |
|
| 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 |
0.489 |
|
| 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 |
0.498 |
|
| 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. DOI: 10.1021/Jp034505Y |
0.604 |
|
| 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 |
0.426 |
|
| 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 |
0.79 |
|
| 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 |
0.65 |
|
| 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 |
0.794 |
|
| 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 |
0.388 |
|
| 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. DOI: 10.1021/Ja993119K |
0.477 |
|
| 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 |
0.35 |
|
| 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 |
0.33 |
|
| 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 DOI: 10.1073/Pnas.92.8.3190 |
0.302 |
|
| 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 |
0.424 |
|
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