| Year |
Citation |
Score |
| 2023 |
Love O, Winkler L, Cheatham TE. van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD. Journal of Chemical Theory and Computation. PMID 38157247 DOI: 10.1021/acs.jctc.3c01164 |
0.409 |
|
| 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, ... ... Cheatham TE, et al. AmberTools. Journal of Chemical Information and Modeling. 63: 6183-6191. PMID 37805934 DOI: 10.1021/acs.jcim.3c01153 |
0.46 |
|
| 2023 |
Love O, Galindo-Murillo R, Zgarbová M, Šponer J, Jurečka P, Cheatham TE. Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition. Journal of Chemical Theory and Computation. PMID 37340948 DOI: 10.1021/acs.jctc.3c00233 |
0.338 |
|
| 2023 |
Winkler L, Cheatham TE. Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide. Journal of Chemical Information and Modeling. PMID 36996447 DOI: 10.1021/acs.jcim.3c00250 |
0.377 |
|
| 2023 |
Winkler L, Galindo-Murillo R, Cheatham TE. Structures and Dynamics of DNA Mini-Dumbbells Are Force Field Dependent. Journal of Chemical Theory and Computation. PMID 36976268 DOI: 10.1021/acs.jctc.3c00130 |
0.385 |
|
| 2022 |
Love O, Pacheco Lima MC, Clark C, Cornillie S, Roalstad S, Cheatham TE. Evaluating the accuracy of the AMBER protein force fields in modeling dihydrofolate reductase structures: misbalance in the conformational arrangements of the flexible loop domains. Journal of Biomolecular Structure & Dynamics. 1-15. PMID 35838167 DOI: 10.1080/07391102.2022.2098823 |
0.343 |
|
| 2022 |
Galindo-Murillo R, Cheatham TE. Transient Hoogsteen Base Pairs Observed in Unbiased Molecular Dynamics Simulations of DNA. The Journal of Physical Chemistry Letters. 6283-6287. PMID 35775742 DOI: 10.1021/acs.jpclett.2c01348 |
0.331 |
|
| 2022 |
Rajasekaran T, Freestone GC, Galindo-Murillo R, Lugato B, Rico L, Salinas JC, Gaus H, Migawa MT, Swayze EE, Cheatham TE, Hanessian S, Seth PP. Backbone Hydrocarbon-Constrained Nucleic Acids Modulate Hybridization Kinetics for RNA. Journal of the American Chemical Society. PMID 35041415 DOI: 10.1021/jacs.1c12323 |
0.333 |
|
| 2021 |
Galindo-Murillo R, Cheatham TE. Ethidium bromide interactions with DNA: an exploration of a classic DNA-ligand complex with unbiased molecular dynamics simulations. Nucleic Acids Research. PMID 33764383 DOI: 10.1093/nar/gkab143 |
0.351 |
|
| 2019 |
Galindo-Murillo R, Cheatham TE. Lessons learned in atomistic simulation of double-stranded DNA: Solvation and salt concerns [Article v1.0]. Living Journal of Computational Molecular Science. 1. PMID 33073182 DOI: 10.33011/livecoms.1.2.9974 |
0.387 |
|
| 2018 |
Roe DR, Cheatham TE. Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data. Journal of Computational Chemistry. 39: 2110-2117. PMID 30368859 DOI: 10.1002/Jcc.25382 |
0.349 |
|
| 2018 |
Galindo-Murillo R, Cheatham TE, Hopkins RC. Exploring potentially alternative non-canonical DNA duplex structures through simulation. Journal of Biomolecular Structure & Dynamics. 1-15. PMID 30047316 DOI: 10.1080/07391102.2018.1483839 |
0.372 |
|
| 2018 |
Chrisman IM, Nemetchek MD, de Vera IMS, Shang J, Heidari Z, Long Y, Reyes-Caballero H, Galindo-Murillo R, Cheatham TE, Blayo AL, Shin Y, Fuhrmann J, Griffin PR, Kamenecka TM, Kojetin DJ, et al. Defining a conformational ensemble that directs activation of PPARγ. Nature Communications. 9: 1794. PMID 29728618 DOI: 10.1038/S41467-018-04176-X |
0.334 |
|
| 2018 |
Cornillie SP, Bruno BJ, Lim CS, Cheatham TE. Computational Modeling of Stapled Peptides Towards a Treatment Strategy for CML and Broader Implications in the Design of Lengthy Peptide Therapeutics. The Journal of Physical Chemistry. B. PMID 29519125 DOI: 10.1021/Acs.Jpcb.8B01014 |
0.347 |
|
| 2018 |
Hayatshahi HS, Henriksen NM, Cheatham TE. Consensus conformations of dinucleotide monophosphates described with well-converged molecular dynamics simulations. Journal of Chemical Theory and Computation. PMID 29323894 DOI: 10.1021/Acs.Jctc.7B00581 |
0.759 |
|
| 2017 |
Galindo-Murillo R, Cheatham TE. Computational DNA binding studies of (-)-epigallocatechin-3-gallate. Journal of Biomolecular Structure & Dynamics. 1-23. PMID 29059014 DOI: 10.1080/07391102.2017.1389306 |
0.368 |
|
| 2017 |
Bergonzo C, Cheatham TE. Mg(2+) Binding Promotes SLV as a Scaffold in Varkud Satellite Ribozyme SLI-SLV Kissing Loop Junction. Biophysical Journal. PMID 28669407 DOI: 10.1016/J.Bpj.2017.06.008 |
0.351 |
|
| 2017 |
Zgarbova M, Jurecka P, Lankas F, Cheatham TE, Sponer J, Otyepka M. Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for all 136 Distinct Tetranucleotide Sequences. Journal of Chemical Information and Modeling. PMID 28059516 DOI: 10.1021/Acs.Jcim.6B00621 |
0.451 |
|
| 2016 |
Hayatshahi HS, Roe DR, Galindo-Murillo R, Hall KB, Cheatham TE. Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in the GTPase-Associating Center RNA. The Journal of Physical Chemistry. B. PMID 27983843 DOI: 10.1021/Acs.Jpcb.6B08764 |
0.346 |
|
| 2016 |
Galindo-Murillo R, Robertson JC, Zgarbova M, Sponer J, Otyepka M, Jurecka P, Cheatham TE. Assessing the current state of AMBER force field modifications for DNA. Journal of Chemical Theory and Computation. PMID 27300587 DOI: 10.1021/Acs.Jctc.6B00186 |
0.488 |
|
| 2016 |
Bergonzo C, Hall KB, Cheatham TE. Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics. Journal of Chemical Theory and Computation. PMID 27294370 DOI: 10.1021/Acs.Jctc.6B00173 |
0.409 |
|
| 2016 |
Heidari Z, Roe DR, Galindo-Murillo R, Ghasemi JB, Cheatham TE. Using Wavelet Analysis to Assist in Identification of Significant Events in Molecular Dynamics Simulations. Journal of Chemical Information and Modeling. PMID 27286268 DOI: 10.1021/Acs.Jcim.5B00727 |
0.345 |
|
| 2016 |
Waters JT, Lu XJ, Galindo-Murillo R, Gumbart JC, Kim HD, Cheatham TE, Harvey SC. Transitions of Double-Stranded DNA Between the A- and B-Forms. The Journal of Physical Chemistry. B. PMID 27135262 DOI: 10.1021/Acs.Jpcb.6B02155 |
0.383 |
|
| 2016 |
Galindo-Murillo R, Davis DR, Cheatham TE. Probing the influence of hypermodified residues within the tRNA3(Lys) anticodon stem loop interacting with the A-loop primer sequence from HIV-1. Biochimica Et Biophysica Acta. 1860: 607-17. PMID 26655694 DOI: 10.1016/J.Bbagen.2015.11.009 |
0.334 |
|
| 2016 |
Bruno BJ, Cornillie SP, Cheatham TE, Chou DH, Lim CS. Abstract 3817: Recombinant stapled proteins for the treatment of chronic myeloid leukemia Cancer Research. 76: 3817-3817. DOI: 10.1158/1538-7445.Am2016-3817 |
0.326 |
|
| 2015 |
Zgarbová M, Šponer J, Otyepka M, Cheatham TE, Galindo-Murillo R, Jurečka P. Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA. Journal of Chemical Theory and Computation. 11: 5723-36. PMID 26588601 DOI: 10.1021/Acs.Jctc.5B00716 |
0.424 |
|
| 2015 |
Robertson JC, Cheatham TE. DNA Backbone BI/BII Distribution and Dynamics in E2 Protein-Bound Environment Determined by Molecular Dynamics Simulations. The Journal of Physical Chemistry. B. 119: 14111-9. PMID 26482568 DOI: 10.1021/Acs.Jpcb.5B08486 |
0.462 |
|
| 2015 |
Bergonzo C, Hall KB, Cheatham TE. Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg(2+) Bound Structure in the Presence of Monovalent Ions. The Journal of Physical Chemistry. B. 119: 12355-64. PMID 26328924 DOI: 10.1021/Acs.Jpcb.5B05190 |
0.382 |
|
| 2015 |
Simmonett AC, Pickard FC, Shao Y, Cheatham TE, Brooks BR. Efficient treatment of induced dipoles. The Journal of Chemical Physics. 143: 074115. PMID 26298123 DOI: 10.1063/1.4928530 |
0.516 |
|
| 2015 |
Bergonzo C, Henriksen NM, Roe DR, Cheatham TE. Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields. Rna (New York, N.Y.). 21: 1578-90. PMID 26124199 DOI: 10.1261/Rna.051102.115 |
0.762 |
|
| 2015 |
Cheatham T. 41 A full exploration of the conformational ensembles of nucleic acid structural motifs. Journal of Biomolecular Structure & Dynamics. 33: 28. PMID 26103252 DOI: 10.1080/07391102.2015.1032590 |
0.396 |
|
| 2015 |
Galindo-Murillo R, García-Ramos JC, Ruiz-Azuara L, Cheatham TE, Cortés-Guzmán F. Intercalation processes of copper complexes in DNA. Nucleic Acids Research. 43: 5364-76. PMID 25958394 DOI: 10.1093/Nar/Gkv467 |
0.359 |
|
| 2015 |
Galindo-Murillo R, Roe DR, Cheatham TE. Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC). Biochimica Et Biophysica Acta. 1850: 1041-58. PMID 25219455 DOI: 10.1016/J.Bbagen.2014.09.007 |
0.443 |
|
| 2015 |
Cheatham TE, Roe DR. The impact of heterogeneous computing on workflows for biomolecular simulation and analysis Computing in Science and Engineering. 17: 30-39. DOI: 10.1109/Mcse.2015.7 |
0.4 |
|
| 2015 |
Galindo-Murillo R, Cheatham TE. 129 Convergence and reproducibility of the DNA duplex d(GCACGAACGAACGAACGC) using molecular dynamics simulations Journal of Biomolecular Structure & Dynamics. 33: 83-84. DOI: 10.1080/07391102.2015.1032762 |
0.414 |
|
| 2014 |
Bergonzo C, Galindo-Murillo R, Cheatham TE. Molecular modeling of nucleic Acid structure: electrostatics and solvation. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. 55: 7.9.1-7.9.27. PMID 25631536 DOI: 10.1002/0471142700.nc0709s55 |
0.356 |
|
| 2014 |
Galindo-Murillo R, Bergonzo C, Cheatham TE. Molecular modeling of nucleic Acid structure: setup and analysis. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. 56: 7.10.1-7.10.21. PMID 25606980 DOI: 10.1002/0471142700.nc0710s56 |
0.362 |
|
| 2014 |
Galindo-Murillo R, Roe DR, Cheatham TE. On the absence of intrahelical DNA dynamics on the μs to ms timescale. Nature Communications. 5: 5152. PMID 25351257 DOI: 10.1038/Ncomms6152 |
0.345 |
|
| 2014 |
Pasi M, Maddocks JH, Beveridge D, Bishop TC, Case DA, Cheatham T, Dans PD, Jayaram B, Lankas F, Laughton C, Mitchell J, Osman R, Orozco M, Pérez A, Petkevi?i?t? D, et al. μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acids Research. 42: 12272-83. PMID 25260586 DOI: 10.1093/Nar/Gku855 |
0.396 |
|
| 2014 |
Stadlbauer P, Trantírek L, Cheatham TE, Ko?a J, Sponer J. Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations. Biochimie. 105: 22-35. PMID 25038568 DOI: 10.1016/J.Biochi.2014.07.009 |
0.459 |
|
| 2014 |
Henriksen NM, Hayatshahi HS, Davis DR, Cheatham TE. Structural and energetic analysis of 2-aminobenzimidazole inhibitors in complex with the hepatitis C virus IRES RNA using molecular dynamics simulations. Journal of Chemical Information and Modeling. 54: 1758-72. PMID 24835734 DOI: 10.1021/Ci500132C |
0.743 |
|
| 2014 |
Thibault JC, Cheatham TE, Facelli JC. iBIOMES Lite: summarizing biomolecular simulation data in limited settings. Journal of Chemical Information and Modeling. 54: 1810-9. PMID 24830957 DOI: 10.1021/Ci500173W |
0.316 |
|
| 2014 |
Galindo-Murillo R, Cheatham TE. DNA binding dynamics and energetics of cobalt, nickel, and copper metallopeptides. Chemmedchem. 9: 1252-9. PMID 24799395 DOI: 10.1002/Cmdc.201402020 |
0.37 |
|
| 2014 |
Roe DR, Bergonzo C, Cheatham TE. Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methods. The Journal of Physical Chemistry. B. 118: 3543-52. PMID 24625009 DOI: 10.1021/Jp4125099 |
0.382 |
|
| 2014 |
Thibault JC, Roe DR, Facelli JC, Cheatham TE. Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing. Journal of Cheminformatics. 6: 4. PMID 24484917 DOI: 10.1186/1758-2946-6-4 |
0.323 |
|
| 2014 |
Bergonzo C, Henriksen NM, Roe DR, Swails JM, Roitberg AE, Cheatham TE. Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide. Journal of Chemical Theory and Computation. 10: 492-499. PMID 24453949 DOI: 10.1021/Ct400862K |
0.755 |
|
| 2013 |
Roe DR, Cheatham TE. PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data. Journal of Chemical Theory and Computation. 9: 3084-95. PMID 26583988 DOI: 10.1021/Ct400341P |
0.315 |
|
| 2013 |
Bergonzo C, Galindo-Murillo R, Cheatham TE. Molecular modeling of nucleic acid structure: energy and sampling. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. 54: Unit 7.8.. PMID 24510800 DOI: 10.1002/0471142700.nc0708s54 |
0.322 |
|
| 2013 |
Galindo-Murillo R, Bergonzo C, Cheatham TE. Molecular modeling of nucleic acid structure. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. 54: Unit 7.5.. PMID 24510799 DOI: 10.1002/0471142700.Nc0705S54 |
0.408 |
|
| 2013 |
Zgarbová M, Luque FJ, Sponer J, Cheatham TE, Otyepka M, Jurečka P. Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. Journal of Chemical Theory and Computation. 9: 2339-2354. PMID 24058302 DOI: 10.1021/Ct400154J |
0.45 |
|
| 2013 |
Cheatham TE, Case DA. Twenty-five years of nucleic acid simulations. Biopolymers. 99: 969-77. PMID 23784813 DOI: 10.1002/Bip.22331 |
0.471 |
|
| 2013 |
Šponer J, Mládek A, Špačková N, Cang X, Cheatham TE, Grimme S. Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations. Journal of the American Chemical Society. 135: 9785-96. PMID 23742743 DOI: 10.1021/Ja402525C |
0.711 |
|
| 2013 |
Stadlbauer P, Krepl M, Cheatham TE, Koca J, Sponer J. Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations. Nucleic Acids Research. 41: 7128-43. PMID 23700306 DOI: 10.1093/Nar/Gkt412 |
0.435 |
|
| 2013 |
Henriksen NM, Roe DR, Cheatham TE. Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations. The Journal of Physical Chemistry. B. 117: 4014-27. PMID 23477537 DOI: 10.1021/Jp400530E |
0.77 |
|
| 2013 |
Thibault JC, Facelli JC, Cheatham TE. iBIOMES: managing and sharing biomolecular simulation data in a distributed environment. Journal of Chemical Information and Modeling. 53: 726-36. PMID 23413948 DOI: 10.1021/Ci300524J |
0.32 |
|
| 2013 |
Zgarbová M, Otyepka M, Banáš P, Luque FJ, Cheatham TE, Šponer J, Jurečka P. 110 Refinement of force field torsion parameters for nucleic acids based on inclusion of conformation-dependent solvation effects Journal of Biomolecular Structure and Dynamics. 31: 70-70. DOI: 10.1080/07391102.2013.786352 |
0.444 |
|
| 2012 |
Krepl M, Zgarbová M, Stadlbauer P, Otyepka M, Banáš P, Koča J, Cheatham TE, Jurečka P, Sponer J. Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA. Journal of Chemical Theory and Computation. 8: 2506-2520. PMID 23197943 DOI: 10.1021/Ct300275S |
0.431 |
|
| 2012 |
Beveridge DL, Cheatham TE, Mezei M. The ABCs of molecular dynamics simulations on B-DNA, circa 2012. Journal of Biosciences. 37: 379-97. PMID 22750978 DOI: 10.1007/S12038-012-9222-6 |
0.469 |
|
| 2012 |
Henriksen NM, Davis DR, Cheatham TE. Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure. Journal of Biomolecular Nmr. 53: 321-39. PMID 22714631 DOI: 10.1007/S10858-012-9642-5 |
0.775 |
|
| 2012 |
Sponer J, Cang X, Cheatham TE. Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures. Methods (San Diego, Calif.). 57: 25-39. PMID 22525788 DOI: 10.1016/J.Ymeth.2012.04.005 |
0.729 |
|
| 2012 |
Lin Z, Flores M, Forteza I, Henriksen NM, Concepcion GP, Rosenberg G, Haygood MG, Olivera BM, Light AR, Cheatham TE, Schmidt EW. Totopotensamides, polyketide-cyclic peptide hybrids from a mollusk-associated bacterium Streptomyces sp. Journal of Natural Products. 75: 644-9. PMID 22439622 DOI: 10.1021/Np200886X |
0.687 |
|
| 2012 |
Dixon AS, Miller GD, Bruno BJ, Constance JE, Woessner DW, Fidler TP, Robertson JC, Cheatham TE, Lim CS. Improved coiled-coil design enhances interaction with Bcr-Abl and induces apoptosis. Molecular Pharmaceutics. 9: 187-95. PMID 22136227 DOI: 10.1021/Mp200461S |
0.318 |
|
| 2012 |
Shahrokh K, Orendt A, Yost GS, Cheatham TE. Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle. Journal of Computational Chemistry. 33: 119-33. PMID 21997754 DOI: 10.1002/Jcc.21922 |
0.326 |
|
| 2011 |
Zgarbová M, Otyepka M, Sponer J, Mládek A, Banáš P, Cheatham TE, Jurečka P. Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. Journal of Chemical Theory and Computation. 7: 2886-2902. PMID 21921995 DOI: 10.1021/Ct200162X |
0.45 |
|
| 2011 |
Cang X, Šponer J, Cheatham TE. Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis. Journal of the American Chemical Society. 133: 14270-9. PMID 21761922 DOI: 10.1021/Ja107805R |
0.693 |
|
| 2011 |
Dixon AS, Pendley SS, Bruno BJ, Woessner DW, Shimpi AA, Cheatham TE, Lim CS. Disruption of Bcr-Abl coiled coil oligomerization by design. The Journal of Biological Chemistry. 286: 27751-60. PMID 21659527 DOI: 10.1074/Jbc.M111.264903 |
0.728 |
|
| 2011 |
Wei X, Henriksen NM, Skalicky JJ, Harper MK, Cheatham TE, Ireland CM, Van Wagoner RM. Araiosamines A-D: tris-bromoindole cyclic guanidine alkaloids from the marine sponge Clathria (Thalysias) araiosa. The Journal of Organic Chemistry. 76: 5515-23. PMID 21462976 DOI: 10.1021/Jo200327D |
0.684 |
|
| 2011 |
Cang X, Šponer J, Cheatham TE. Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes. Nucleic Acids Research. 39: 4499-512. PMID 21296760 DOI: 10.1093/Nar/Gkr031 |
0.653 |
|
| 2011 |
DeMille RC, Cheatham TE, Molinero V. A coarse-grained model of DNA with explicit solvation by water and ions. The Journal of Physical Chemistry. B. 115: 132-42. PMID 21155552 DOI: 10.1021/Jp107028N |
0.342 |
|
| 2010 |
Banáš P, Hollas D, Zgarbová M, Jurečka P, Orozco M, Cheatham TE, Šponer J, Otyepka M. Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins. Journal of Chemical Theory and Computation. 6: 3836-3849. PMID 35283696 DOI: 10.1021/ct100481h |
0.355 |
|
| 2010 |
Moore CD, Shahrokh K, Sontum SF, Cheatham TE, Yost GS. Improved cytochrome P450 3A4 molecular models accurately predict the Phe215 requirement for raloxifene dehydrogenation selectivity. Biochemistry. 49: 9011-9. PMID 20812728 DOI: 10.1021/Bi101139Q |
0.32 |
|
| 2010 |
Paulsen RB, Seth PP, Swayze EE, Griffey RH, Skalicky JJ, Cheatham TE, Davis DR. Inhibitor-induced structural change in the HCV IRES domain IIa RNA. Proceedings of the National Academy of Sciences of the United States of America. 107: 7263-8. PMID 20360559 DOI: 10.1073/Pnas.0911896107 |
0.357 |
|
| 2010 |
Freedman H, Huynh LP, Le L, Cheatham TE, Tuszynski JA, Truong TN. Explicitly solvated ligand contribution to continuum solvation models for binding free energies: selectivity of theophylline binding to an RNA aptamer. The Journal of Physical Chemistry. B. 114: 2227-37. PMID 20099932 DOI: 10.1021/Jp9059664 |
0.365 |
|
| 2010 |
Lavery R, Zakrzewska K, Beveridge D, Bishop TC, Case DA, Cheatham T, Dixit S, Jayaram B, Lankas F, Laughton C, Maddocks JH, Michon A, Osman R, Orozco M, Perez A, et al. A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic Acids Research. 38: 299-313. PMID 19850719 DOI: 10.1093/Nar/Gkp834 |
0.424 |
|
| 2010 |
Banáš P, Hollas D, Zgarbová M, Jurečka P, Orozco M, Cheatham TE, Šponer J, Otyepka M. Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins Journal of Chemical Theory and Computation. 6: 3836-3849. DOI: 10.1021/Ct100481H |
0.441 |
|
| 2009 |
Fadrná E, Špačková N, Sarzyñska J, Koča J, Orozco M, Cheatham TE, Kulinski T, Šponer J. Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields. Journal of Chemical Theory and Computation. 5: 2514-30. PMID 26616629 DOI: 10.1021/Ct900200K |
0.516 |
|
| 2009 |
Joung IS, Persil Cetinkol O, Hud NV, Cheatham TE. Molecular dynamics simulations and coupled nucleotide substitution experiments indicate the nature of A{middle dot}A base pairing and a putative structure of the coralyne-induced homo-adenine duplex. Nucleic Acids Research. 37: 7715-27. PMID 19850721 DOI: 10.1093/Nar/Gkp730 |
0.403 |
|
| 2009 |
Joung IS, Cheatham TE. Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters. The Journal of Physical Chemistry. B. 113: 13279-90. PMID 19757835 DOI: 10.1021/Jp902584C |
0.351 |
|
| 2009 |
Pendley SS, Yu YB, Cheatham TE. Molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coils. Proteins. 74: 612-29. PMID 18704948 DOI: 10.1002/Prot.22177 |
0.779 |
|
| 2009 |
Wang H, Cheatham TE, Gannett PM, Lewis JP. Differential electronic states observed during A-B DNA duplex conformational transitions Soft Matter. 5: 685-690. DOI: 10.1039/B800462E |
0.437 |
|
| 2008 |
Joung IS, Cheatham TE. Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. The Journal of Physical Chemistry. B. 112: 9020-41. PMID 18593145 DOI: 10.1021/Jp8001614 |
0.333 |
|
| 2008 |
Svozil D, Sponer JE, Marchan I, Pérez A, Cheatham TE, Forti F, Luque FJ, Orozco M, Sponer J. Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids. The Journal of Physical Chemistry. B. 112: 8188-97. PMID 18558755 DOI: 10.1021/Jp801245H |
0.412 |
|
| 2007 |
Auffinger P, Cheatham TE, Vaiana AC. Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue? Journal of Chemical Theory and Computation. 3: 1851-9. PMID 26627627 DOI: 10.1021/Ct700143S |
0.41 |
|
| 2007 |
Wierzbicki A, Dalal P, Cheatham TE, Knickelbein JE, Haymet AD, Madura JD. Antifreeze proteins at the ice/water interface: three calculated discriminating properties for orientation of type I proteins. Biophysical Journal. 93: 1442-51. PMID 17526572 DOI: 10.1529/Biophysj.107.105189 |
0.32 |
|
| 2007 |
Pérez A, Marchán I, Svozil D, Sponer J, Cheatham TE, Laughton CA, Orozco M. Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophysical Journal. 92: 3817-29. PMID 17351000 DOI: 10.1529/Biophysj.106.097782 |
0.438 |
|
| 2006 |
Paesani F, Zhang W, Case DA, Cheatham TE, Voth GA. An accurate and simple quantum model for liquid water. The Journal of Chemical Physics. 125: 184507. PMID 17115765 DOI: 10.1063/1.2386157 |
0.364 |
|
| 2006 |
Cheatham TE, Case DA. Using AMBER to simulate DNA and RNA Computational Studies of Rna and Dna. 45-71. DOI: 10.1007/978-1-4020-4851-3_2 |
0.384 |
|
| 2006 |
Špačková N, Cheatham TE, Šponer J. Molecular dynamics simulations of nucleic acids Computational Studies of Rna and Dna. 301-325. DOI: 10.1007/978-1-4020-4851-3_12 |
0.369 |
|
| 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 |
0.329 |
|
| 2005 |
Dixit SB, Beveridge DL, Case DA, Cheatham TE, Giudice E, Lankas F, Lavery R, Maddocks JH, Osman R, Sklenar H, Thayer KM, Varnai P. Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps. Biophysical Journal. 89: 3721-40. PMID 16169978 DOI: 10.1529/Biophysj.105.067397 |
0.446 |
|
| 2005 |
Cheatham TE. Chapter 6 Molecular Modeling and Atomistic Simulation of Nucleic Acids Annual Reports in Computational Chemistry. 1: 75-89. DOI: 10.1016/S1574-1400(05)01006-6 |
0.497 |
|
| 2004 |
Beveridge DL, Barreiro G, Byun KS, Case DA, Cheatham TE, Dixit SB, Giudice E, Lankas F, Lavery R, Maddocks JH, Osman R, Seibert E, Sklenar H, Stoll G, Thayer KM, et al. Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps. Biophysical Journal. 87: 3799-813. PMID 15326025 DOI: 10.1529/Biophysj.104.045252 |
0.447 |
|
| 2004 |
Fadrná E, Spacková N, Stefl R, Koca J, Cheatham TE, Sponer J. Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations. Biophysical Journal. 87: 227-42. PMID 15240460 DOI: 10.1529/Biophysj.103.034751 |
0.509 |
|
| 2004 |
Cheatham TE. Simulation and modeling of nucleic acid structure, dynamics and interactions. Current Opinion in Structural Biology. 14: 360-7. PMID 15193317 DOI: 10.1016/J.Sbi.2004.05.001 |
0.474 |
|
| 2004 |
Lankas F, Sponer J, Langowski J, Cheatham TE. DNA deformability at the base pair level. Journal of the American Chemical Society. 126: 4124-5. PMID 15053599 DOI: 10.1021/Ja0390449 |
0.43 |
|
| 2003 |
Lankas F, Sponer J, Langowski J, Cheatham TE. DNA basepair step deformability inferred from molecular dynamics simulations. Biophysical Journal. 85: 2872-83. PMID 14581192 DOI: 10.1016/S0006-3495(03)74710-9 |
0.43 |
|
| 2003 |
Stefl R, Cheatham TE, Spacková N, Fadrná E, Berger I, Koca J, Sponer J. Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates. Biophysical Journal. 85: 1787-804. PMID 12944293 DOI: 10.1016/S0006-3495(03)74608-6 |
0.438 |
|
| 2003 |
Spacková N, Cheatham TE, Ryjácek F, Lankas F, Van Meervelt L, Hobza P, Sponer J. Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and DNA duplexes in solution. Journal of the American Chemical Society. 125: 1759-69. PMID 12580601 DOI: 10.1021/Ja025660D |
0.443 |
|
| 2003 |
Lewis JP, Cheatham TE, Starikov EB, Wang H, Sankey OF. Dynamically amorphous character of electronic states in poly(dA)-poly(dT) DNA Journal of Physical Chemistry B. 107: 2581-2587. DOI: 10.1021/Jp026772U |
0.413 |
|
| 2002 |
Lankas F, Cheatham TE, Spacková N, Hobza P, Langowski J, Sponer J. Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts. Biophysical Journal. 82: 2592-609. PMID 11964246 DOI: 10.1016/S0006-3495(02)75601-4 |
0.48 |
|
| 2001 |
Cheatham TE, Brooks BR, Kollman PA. Molecular modeling of nucleic acid structure: electrostatics and solvation. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 7.9. PMID 18428877 DOI: 10.1002/0471142700.Nc0709S05 |
0.659 |
|
| 2001 |
Cheatham TE, Brooks BR, Kollman PA. Molecular modeling of nucleic acid structure: energy and sampling. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 7.8. PMID 18428876 DOI: 10.1002/0471142700.Nc0708S04 |
0.666 |
|
| 2001 |
Cheatham TE, Brooks BR, Kollman PA. Molecular modeling of nucleic acid structure. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 7.5. PMID 18428873 DOI: 10.1002/0471142700.Nc0705S06 |
0.658 |
|
| 2001 |
Cheatham TE, Brooks BR, Kollman PA. Molecular modeling of nucleic acid structure: setup and analysis. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 7.10. PMID 18428869 DOI: 10.1002/0471142700.Nc0710S06 |
0.692 |
|
| 2000 |
Cheatham TE, Young MA. Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise Biopolymers. 56: 232-256. PMID 11754338 DOI: 10.1002/1097-0282(2000)56:4<232::Aid-Bip10037>3.0.Co;2-H |
0.508 |
|
| 2000 |
Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Accounts of Chemical Research. 33: 889-97. PMID 11123888 DOI: 10.1021/Ar000033J |
0.792 |
|
| 2000 |
Cheatham TE, Kollman PA. Molecular dynamics simulation of nucleic acids. Annual Review of Physical Chemistry. 51: 435-71. PMID 11031289 DOI: 10.1146/Annurev.Physchem.51.1.435 |
0.613 |
|
| 2000 |
Cheatham TE, Young MA. Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise* We would like to dedicate this article to Peter Kollman, a friend, collaborator, mentor, and all around good guy. Peter was very enthusiastic about DNA simulation; he will be sorely missed. Biopolymers. 56: 232. DOI: 10.1002/1097-0282(2000)56:4<232::Aid-Bip10037>3.3.Co;2-8 |
0.444 |
|
| 1999 |
Cheatham TE, Cieplak P, Kollman PA. A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. Journal of Biomolecular Structure & Dynamics. 16: 845-62. PMID 10217454 DOI: 10.1080/07391102.1999.10508297 |
0.535 |
|
| 1999 |
Konerding DE, Cheatham TE, Kollman PA, James TL. Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method. Journal of Biomolecular Nmr. 13: 119-31. PMID 10070753 DOI: 10.1023/A:1008353423074 |
0.629 |
|
| 1998 |
Cheatham TE, Srinivasan J, Case DA, Kollman PA. Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. Journal of Biomolecular Structure & Dynamics. 16: 265-80. PMID 9833666 DOI: 10.1080/07391102.1998.10508245 |
0.622 |
|
| 1998 |
Bogusz S, Cheatham TE, Brooks BR. Removal of pressure and free energy artifacts in charged periodic systems via net charge corrections to the Ewald potential The Journal of Chemical Physics. 108: 7070-7084. DOI: 10.1063/1.476320 |
0.476 |
|
| 1998 |
Srinivasan J, Cheatham TE, Cieplak P, Kollman PA, Case DA. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices Journal of the American Chemical Society. 120: 9401-9409. DOI: 10.1021/Ja981844+ |
0.584 |
|
| 1998 |
Harvey SC, Tan RK, Cheatham TE. The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition Journal of Computational Chemistry. 19: 726-740. DOI: 10.1002/(Sici)1096-987X(199805)19:7<726::Aid-Jcc4>3.0.Co;2-S |
0.381 |
|
| 1998 |
Cheatham TE, Brooks BR. Recent advances in molecular dynamics simulation towards the realistic representation of biomolecules in solution Theoretical Chemistry Accounts. 99: 279-288. |
0.418 |
|
| 1998 |
Cheatham TE, Miller JL, Spector TI, Cieplak P, Kollman PA. Molecular Dynamics Simulations on Nucleic Acid Systems Using the Cornell et al. Force Field and Particle Mesh Ewald Electrostatics Acs Symposium Series. 682: 285-303. |
0.488 |
|
| 1997 |
Cheatham TE, Kollman PA. Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III). Structure (London, England : 1993). 5: 1297-311. PMID 9351805 DOI: 10.1016/S0969-2126(97)00282-7 |
0.583 |
|
| 1997 |
Cheatham TE, Crowley MF, Fox T, Kollman PA. A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions. Proceedings of the National Academy of Sciences of the United States of America. 94: 9626-30. PMID 9275173 DOI: 10.1073/Pnas.94.18.9626 |
0.541 |
|
| 1997 |
Crowley MF, Darden TA, Cheatham TE, Deerfield DW. Adventures in Improving the Scaling and Accuracy of a Parallel Molecular Dynamics Program Journal of Supercomputing. 11: 255-278. DOI: 10.1023/A:1007907925007 |
0.326 |
|
| 1997 |
Spector TI, Cheatham TE, Kollman PA. Unrestrained molecular dynamics of photodamaged DNA in aqueous solution Journal of the American Chemical Society. 119: 7095-7104. DOI: 10.1021/Ja964372C |
0.572 |
|
| 1997 |
Cieplak P, Cheatham TE, Kollman PA. Molecular dynamics simulations find that 3' phosphoramidate modified DNA duplexes undergo a B to A transition and normal DNA duplexes an A to B transition Journal of the American Chemical Society. 119: 6722-6730. DOI: 10.1021/Ja963909J |
0.578 |
|
| 1997 |
Cheatham TE, Kollman PA. Molecular dynamics simulations highlight the structural differences among DNA:DNA, RNA:RNA, and DNA:RNA hybrid duplexes Journal of the American Chemical Society. 119: 4805-4825. DOI: 10.1021/Ja963641W |
0.57 |
|
| 1996 |
Cheatham TE, Kollman PA. Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution. Journal of Molecular Biology. 259: 434-44. PMID 8676379 DOI: 10.1006/Jmbi.1996.0330 |
0.595 |
|
| 1995 |
Cheatham TE, Miller JL, Fox T, Darden TA, Kollman PA. Molecular dynamics simulations on solvated biomolecular systems: The particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins Journal of the American Chemical Society. 117: 4193-4194. DOI: 10.1021/Ja00119A045 |
0.576 |
|
| 1995 |
Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, DeBolt S, Ferguson D, Seibel G, Kollman P. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules Computer Physics Communications. 91: 1-41. DOI: 10.1016/0010-4655(95)00041-D |
0.533 |
|
| Show low-probability matches. |