Thomas E. Cheatham - Publications

Affiliations: 
Medicinal Chemistry University of Utah, Salt Lake City, UT 
Area:
Pharmaceutical Chemistry, Biochemistry, General Biophysics

113 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, 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
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  0.56
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  0.36
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  0.68
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  0.48
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  0.68
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  0.84
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  0.84
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  0.84
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  0.84
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  0.56
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 - General Subjects. 1860: 607-617. DOI: 10.1016/j.bbagen.2015.11.009  0.56
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  0.84
2015 Bergonzo C, Iii TE. Improved Force Field Parameters Lead to a Better Description of RNA Structure. Journal of Chemical Theory and Computation. 11: 3969-72. PMID 26575892 DOI: 10.1021/acs.jctc.5b00444  0.84
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  0.84
2015 Thibault JC, Roe DR, Eilbeck K, Cheatham Iii TE, Facelli JC. Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology. Sar and Qsar in Environmental Research. 26: 577-93. PMID 26387907 DOI: 10.1080/1062936X.2015.1076515  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
2015 Galindo-Murillo R, Cheatham TE. Using Information about DNA Structure and Dynamics from Experiment and Simulation to Give Insight into Genome-Wide Association Studies Translational Cardiometabolic Genomic Medicine. 83-98. DOI: 10.1016/B978-0-12-799961-6.00004-4  0.84
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  0.84
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  0.84
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  0.84
2014 Lin Z, Koch M, Abdel Aziz MH, Galindo-Murillo R, Tianero MD, Cheatham TE, Barrows LR, Reilly CA, Schmidt EW. Oxazinin A, a pseudodimeric natural product of mixed biosynthetic origin from a filamentous fungus. Organic Letters. 16: 4774-7. PMID 25188821 DOI: 10.1021/ol502227x  0.84
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  0.84
2014 Okal A, Cornillie S, Matissek SJ, Matissek KJ, Cheatham TE, Lim CS. Re-engineered p53 chimera with enhanced homo-oligomerization that maintains tumor suppressor activity. Molecular Pharmaceutics. 11: 2442-52. PMID 24836513 DOI: 10.1021/mp500202p  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
2013 Ashton NN, Roe DR, Weiss RB, Cheatham TE, Stewart RJ. Self-tensioning aquatic caddisfly silk: Ca2+-dependent structure, strength, and load cycle hysteresis. Biomacromolecules. 14: 3668-81. PMID 24050221 DOI: 10.1021/bm401036z  0.84
2013 Cheatham TE, Case DA. Twenty-five years of nucleic acid simulations. Biopolymers. 99: 969-77. PMID 23784813 DOI: 10.1002/bip.22331  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
2012 Shahrokh K, Cheatham TE, Yost GS. Conformational dynamics of CYP3A4 demonstrate the important role of Arg212 coupled with the opening of ingress, egress and solvent channels to dehydrogenation of 4-hydroxy-tamoxifen. Biochimica Et Biophysica Acta. 1820: 1605-17. PMID 22677141 DOI: 10.1016/j.bbagen.2012.05.011  0.84
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  0.84
2012 Dixon AS, Miller GD, Bruno BJ, Constance JE, Woessner DW, Fidler TP, Robertson JC, Cheatham TE, Lim CS. Correction to "improved coiled-coil design enhances interaction with bcr-abl and induces apoptosis". Molecular Pharmaceutics. 9: 1535. PMID 22444272 DOI: 10.1021/mp300089a  0.36
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
2011 Thomas KC, Ethirajan M, Shahrokh K, Sun H, Lee J, Cheatham TE, Yost GS, Reilly CA. Structure-activity relationship of capsaicin analogs and transient receptor potential vanilloid 1-mediated human lung epithelial cell toxicity. The Journal of Pharmacology and Experimental Therapeutics. 337: 400-10. PMID 21343315 DOI: 10.1124/jpet.110.178491  0.84
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  0.84
2011 Demille RC, Cheatham TE, Molinero V. A coarse-grained model of DNA with explicit solvation by water and ions Journal of Physical Chemistry B. 115: 132-142. DOI: 10.1021/jp107028n  0.84
2010 Wong KF, Sonnenberg JL, Paesani F, Yamamoto T, Vaní?ek J, Zhang W, Schlegel HB, Case DA, Cheatham TE, Miller WH, Voth GA. Proton Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology. Journal of Chemical Theory and Computation. 6: 2566-2580. PMID 21116485 DOI: 10.1021/ct900579k  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
2009 Han TS, Zhang MM, Walewska A, Gruszczynski P, Robertson CR, Cheatham TE, Yoshikami D, Olivera BM, Bulaj G. Structurally minimized mu-conotoxin analogues as sodium channel blockers: implications for designing conopeptide-based therapeutics. Chemmedchem. 4: 406-14. PMID 19107760 DOI: 10.1002/cmdc.200800292  0.84
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  0.84
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  0.84
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  0.84
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  0.84
2007 Shao J, Tanner SW, Thompson N, Cheatham TE. Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms. Journal of Chemical Theory and Computation. 3: 2312-34. PMID 26636222 DOI: 10.1021/ct700119m  0.84
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  0.84
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  0.84
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  0.84
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  0.84
2006 Truong TN, Nayak M, Huynh HH, Cook T, Mahajan P, Tran LT, Bharath J, Jain S, Pham HB, Boonyasiriwat C, Nguyen N, Andersen E, Kim Y, Choe S, Choi J, ... Cheatham TE, et al. Computational Science and Engineering Online (CSE-Online): a cyber-infrastructure for scientific computing. Journal of Chemical Information and Modeling. 46: 971-84. PMID 16711715 DOI: 10.1021/ci0503917  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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+  0.84
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.  0.84
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 Journal of Chemical Physics. 108: 7070-7084.  0.84
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.  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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.  0.84
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  0.84
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  0.84
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.  0.84
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