Thomas E Cheatham

Thomas E Cheatham

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Thomas E Cheatham

Thomas E Cheatham

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Exploring potentially alternative non-canonical DNA duplex structures through simulation.

J Biomol Struct Dyn 2019 Jun 17;37(9):2201-2210. Epub 2018 Nov 17.

a Department of Medicinal Chemistry , L. S. Skaggs Pharmacy Institute, University of Utah , Salt Lake City , UT , USA.

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http://dx.doi.org/10.1080/07391102.2018.1483839DOI Listing
June 2019

Computational DNA binding studies of (-)-epigallocatechin-3-gallate.

J Biomol Struct Dyn 2018 Oct 3;36(13):3311-3323. Epub 2017 Nov 3.

a Department of Medicinal Chemistry , L. S. Skaggs Pharmacy Institute, University of Utah , Salt Lake City , UT 84112 , USA.

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http://dx.doi.org/10.1080/07391102.2017.1389306DOI Listing
October 2018

Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data.

J Comput Chem 2018 09 3;39(25):2110-2117. Epub 2018 Oct 3.

T. E. Cheatham Department of Medicinal Chemistry, College of Pharmacy, 2000 South 30 East Room 105, University of Utah, Salt Lake City, Utah, 84112.

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http://doi.wiley.com/10.1002/jcc.25382
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http://dx.doi.org/10.1002/jcc.25382DOI Listing
September 2018

Consensus Conformations of Dinucleoside Monophosphates Described with Well-Converged Molecular Dynamics Simulations.

J Chem Theory Comput 2018 Mar 6;14(3):1456-1470. Epub 2018 Feb 6.

Department of Medicinal Chemistry, College of Pharmacy, L. S. Skaggs Pharmacy Research Institute , University of Utah , Salt Lake City , Utah 84112-5820 , United States.

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http://dx.doi.org/10.1021/acs.jctc.7b00581DOI Listing
March 2018

Investigating the ion dependence of the first unfolding step of GTPase-Associating Center ribosomal RNA.

J Biomol Struct Dyn 2018 01 13;36(1):243-253. Epub 2017 Apr 13.

a Department of Medicinal Chemistry , College of Pharmacy, The University of Utah , 2000 East 30 South Skaggs 307, Salt Lake City , Utah 84112-5820 , USA.

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http://dx.doi.org/10.1080/07391102.2016.1274272DOI Listing
January 2018

Mg Binding Promotes SLV as a Scaffold in Varkud Satellite Ribozyme SLI-SLV Kissing Loop Junction.

Biophys J 2017 Jul 29;113(2):313-320. Epub 2017 Jun 29.

University of Utah, Salt Lake City, Utah. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2017.06.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529310PMC
July 2017

Application of Thiol-yne/Thiol-ene Reactions for Peptide and Protein Macrocyclizations.

Chemistry 2017 May 26;23(29):7087-7092. Epub 2017 Apr 26.

Department of Biochemistry, University of Utah, 15 N, Medical Drive East 4100, Salt Lake City, UT, 84112, USA.

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http://dx.doi.org/10.1002/chem.201700572DOI Listing
May 2017

Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences.

J Chem Inf Model 2017 02 20;57(2):275-287. Epub 2017 Jan 20.

Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17 listopadu 12, 77146 Olomouc, Czech Republic.

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http://dx.doi.org/10.1021/acs.jcim.6b00621DOI Listing
February 2017

Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA.

J Phys Chem B 2017 01 17;121(3):451-462. Epub 2017 Jan 17.

Department of Medicinal Chemistry, College of Pharmacy, The University of Utah , 2000 East 30 South Skaggs 307, Salt Lake City, Utah 84112-5820, United States.

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http://pubs.acs.org/doi/10.1021/acs.jpcb.6b08764
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http://dx.doi.org/10.1021/acs.jpcb.6b08764DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5278497PMC
January 2017

Molecular basis for the broad substrate selectivity of a peptide prenyltransferase.

Proc Natl Acad Sci U S A 2016 12 21;113(49):14037-14042. Epub 2016 Nov 21.

Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801;

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http://dx.doi.org/10.1073/pnas.1609869113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5150373PMC
December 2016

Transitions of Double-Stranded DNA Between the A- and B-Forms.

J Phys Chem B 2016 08 11;120(33):8449-56. Epub 2016 May 11.

Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States.

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http://dx.doi.org/10.1021/acs.jpcb.6b02155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5267635PMC
August 2016

Assessing the Current State of Amber Force Field Modifications for DNA.

J Chem Theory Comput 2016 Aug 7;12(8):4114-27. Epub 2016 Jul 7.

Department of Medicinal Chemistry, University of Utah , 2000 East 30 South, Skaggs 105, Salt Lake City, Utah 84112, United States.

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http://dx.doi.org/10.1021/acs.jctc.6b00186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4980684PMC
August 2016

Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations.

J Chem Inf Model 2016 07 22;56(7):1282-91. Epub 2016 Jun 22.

Department of Medicinal Chemistry, L. S. Skaggs Pharmacy Institute, University of Utah , Salt Lake City, Utah 84112, United States.

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http://dx.doi.org/10.1021/acs.jcim.5b00727DOI Listing
July 2016

Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics.

J Chem Theory Comput 2016 Jul 28;12(7):3382-9. Epub 2016 Jun 28.

Department of Medicinal Chemistry, College of Pharmacy, University of Utah , Salt Lake City, Utah 84112, United States.

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http://pubs.acs.org/doi/10.1021/acs.jctc.6b00173
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http://dx.doi.org/10.1021/acs.jctc.6b00173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4944181PMC
July 2016

Probing the influence of hypermodified residues within the tRNA3(Lys) anticodon stem loop interacting with the A-loop primer sequence from HIV-1.

Biochim Biophys Acta 2016 Mar 2;1860(3):607-17. Epub 2015 Dec 2.

Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, United States. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S03044165150032
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http://dx.doi.org/10.1016/j.bbagen.2015.11.009DOI Listing
March 2016

Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA.

J Chem Theory Comput 2015 Dec 20;11(12):5723-36. Epub 2015 Nov 20.

Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17. listopadu 12, 77146 Olomouc, Czech Republic.

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http://pubs.acs.org/doi/10.1021/acs.jctc.5b00716
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http://dx.doi.org/10.1021/acs.jctc.5b00716DOI Listing
December 2015

DNA Backbone BI/BII Distribution and Dynamics in E2 Protein-Bound Environment Determined by Molecular Dynamics Simulations.

J Phys Chem B 2015 Nov 27;119(44):14111-9. Epub 2015 Oct 27.

Department of Medicinal Chemistry, College of Pharmacy, 2000 East 30 South Skaggs 307, The University of Utah , Salt Lake City, Utah 84112-5820, United States.

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http://dx.doi.org/10.1021/acs.jpcb.5b08486DOI Listing
November 2015

Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields.

RNA 2015 Sep 29;21(9):1578-90. Epub 2015 Jun 29.

Department of Medicinal Chemistry, College of Pharmacy, L.S. Skaggs Pharmacy Research Institute, University of Utah, Salt Lake City, Utah 84112, USA.

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http://rnajournal.cshlp.org/lookup/doi/10.1261/rna.051102.11
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http://dx.doi.org/10.1261/rna.051102.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4536319PMC
September 2015

Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg(2+) Bound Structure in the Presence of Monovalent Ions.

J Phys Chem B 2015 Sep 14;119(38):12355-64. Epub 2015 Sep 14.

Department of Medicinal Chemistry, College of Pharmacy, University of Utah , Salt Lake City, Utah 84112, United States.

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http://dx.doi.org/10.1021/acs.jpcb.5b05190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4634716PMC
September 2015

Improved Force Field Parameters Lead to a Better Description of RNA Structure.

J Chem Theory Comput 2015 Sep 18;11(9):3969-72. Epub 2015 Aug 18.

Department of Medicinal Chemistry, College of Pharmacy, University of Utah , Salt Lake City, Utah 84112, United States.

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http://dx.doi.org/10.1021/acs.jctc.5b00444DOI Listing
September 2015

Efficient treatment of induced dipoles.

J Chem Phys 2015 Aug;143(7):074115

Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1063/1.4928530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4545078PMC
August 2015

Intercalation processes of copper complexes in DNA.

Nucleic Acids Res 2015 Jun 9;43(11):5364-76. Epub 2015 May 9.

Instituto de Química, Universidad Nacional Autónoma de México, DF 04510, Mexico Centro Conjunto de Investigación en Química Sustentable UAEMex-UNAM, carretera Toluca-Atlacomulco km 14.5, Toluca, México 50200, Mexico

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http://dx.doi.org/10.1093/nar/gkv467DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477671PMC
June 2015

Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC).

Biochim Biophys Acta 2015 May 16;1850(5):1041-1058. Epub 2014 Sep 16.

Department of Medicinal Chemistry, L.S. Skaggs Pharmacy Institute, University of Utah, Salt Lake City, UT 84112, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bbagen.2014.09.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4339415PMC
May 2015

Molecular modeling of nucleic Acid structure: electrostatics and solvation.

Curr Protoc Nucleic Acid Chem 2014 Dec 19;55:7.9.1-27. Epub 2014 Dec 19.

Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah.

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http://dx.doi.org/10.1002/0471142700.nc0709s55DOI Listing
December 2014

Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations.

Biochimie 2014 Oct 17;105:22-35. Epub 2014 Jul 17.

Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic; CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic. Electronic address:

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http://dx.doi.org/10.1016/j.biochi.2014.07.009DOI Listing
October 2014

On the absence of intrahelical DNA dynamics on the μs to ms timescale.

Nat Commun 2014 Oct 29;5:5152. Epub 2014 Oct 29.

Department of Medicinal Chemistry, L.S. Skaggs Pharmacy Institute, University of Utah, 2000 East 30 South Skaggs 307, Salt Lake City, Utah 84112, USA.

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http://dx.doi.org/10.1038/ncomms6152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4215645PMC
October 2014

Oxazinin A, a pseudodimeric natural product of mixed biosynthetic origin from a filamentous fungus.

Org Lett 2014 Sep 4;16(18):4774-7. Epub 2014 Sep 4.

Department of Medicinal Chemistry and ‡Department of Pharmacology and Toxicology, L. S. Skaggs Pharmacy Institute, University of Utah , Salt Lake City, Utah 84112 United States.

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http://dx.doi.org/10.1021/ol502227xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4168773PMC
September 2014

Re-engineered p53 chimera with enhanced homo-oligomerization that maintains tumor suppressor activity.

Mol Pharm 2014 Jul 29;11(7):2442-52. Epub 2014 May 29.

Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah , Salt Lake City, Utah 84112, United States.

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http://dx.doi.org/10.1021/mp500202pDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114475PMC
July 2014

DNA binding dynamics and energetics of cobalt, nickel, and copper metallopeptides.

ChemMedChem 2014 Jun 2;9(6):1252-9. Epub 2014 May 2.

Department of Medicinal Chemistry, L. S. Skaggs Pharmacy Institute, University of Utah, Salt Lake City, UT 84112 (USA).

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http://dx.doi.org/10.1002/cmdc.201402020DOI Listing
June 2014

iBIOMES Lite: summarizing biomolecular simulation data in limited settings.

J Chem Inf Model 2014 Jun 9;54(6):1810-9. Epub 2014 Jun 9.

Department of Biomedical Informatics and ‡Department of Medicinal Chemistry, University of Utah , Salt Lake City, Utah 84112, United States.

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http://dx.doi.org/10.1021/ci500173wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4076027PMC
June 2014

Structural and energetic analysis of 2-aminobenzimidazole inhibitors in complex with the hepatitis C virus IRES RNA using molecular dynamics simulations.

J Chem Inf Model 2014 Jun 3;54(6):1758-72. Epub 2014 Jun 3.

Department of Medicinal Chemistry, College of Pharmacy, University of Utah , Salt Lake City, Utah 84112, United States.

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http://dx.doi.org/10.1021/ci500132cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4076022PMC
June 2014

Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methods.

J Phys Chem B 2014 Apr 25;118(13):3543-52. Epub 2014 Mar 25.

Department of Medicinal Chemistry, College of Pharmacy, University of Utah , 2000 South 30 East Room 105, Salt Lake City, Utah 84112, United States.

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http://dx.doi.org/10.1021/jp4125099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983400PMC
April 2014

Molecular modeling of nucleic Acid structure: setup and analysis.

Curr Protoc Nucleic Acid Chem 2014 Mar 26;56:7.10.1-21. Epub 2014 Mar 26.

Vanderbilt University; Rega Institute for Medical Research; Hokkaido University; Rasayan Inc.

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http://dx.doi.org/10.1002/0471142700.nc0710s56DOI Listing
March 2014

Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide.

J Chem Theory Comput 2014 Jan 15;10(1):492-499. Epub 2013 Nov 15.

Department of Medicinal Chemistry, College of Pharmacy, University of Utah , Salt Lake City, Utah 84112, United States.

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http://dx.doi.org/10.1021/ct400862kDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893832PMC
January 2014

Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing.

J Cheminform 2014 Jan 30;6(1). Epub 2014 Jan 30.

Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA.

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http://dx.doi.org/10.1186/1758-2946-6-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3915074PMC
January 2014

Twenty-five years of nucleic acid simulations.

Biopolymers 2013 Dec;99(12):969-77

Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 105, Salt Lake City, UT, 84112.

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http://dx.doi.org/10.1002/bip.22331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820278PMC
December 2013

Self-tensioning aquatic caddisfly silk: Ca2+-dependent structure, strength, and load cycle hysteresis.

Biomacromolecules 2013 Oct 3;14(10):3668-81. Epub 2013 Oct 3.

Departments of †Bioengineering, ‡Medicinal Chemistry, and §Human Genetics, University of Utah , Salt Lake City, Utah 84112, United States.

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http://dx.doi.org/10.1021/bm401036zDOI Listing
October 2013

Molecular modeling of nucleic acid structure.

Curr Protoc Nucleic Acid Chem 2013 Oct 8;54:7.5.1-7.5.13. Epub 2013 Oct 8.

Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah.

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http://dx.doi.org/10.1002/0471142700.nc0705s54DOI Listing
October 2013

Molecular modeling of nucleic acid structure: energy and sampling.

Curr Protoc Nucleic Acid Chem 2013 Oct 8;54:7.8.1-7.8.21. Epub 2013 Oct 8.

Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah.

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http://dx.doi.org/10.1002/0471142700.nc0708s54DOI Listing
October 2013

Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations.

Nucleic Acids Res 2013 Aug 21;41(14):7128-43. Epub 2013 May 21.

Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic.

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http://dx.doi.org/10.1093/nar/gkt412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3737530PMC
August 2013

Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations.

J Am Chem Soc 2013 Jul 19;135(26):9785-96. Epub 2013 Jun 19.

Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic.

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http://dx.doi.org/10.1021/ja402525cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3775466PMC
July 2013

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data.

J Chem Theory Comput 2013 Jul 25;9(7):3084-95. Epub 2013 Jun 25.

Department of Medicinal Chemistry, College of Pharmacy, 2000 South 30 East Room 105, University of Utah, Salt Lake City, Utah 84112, United States.

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http://dx.doi.org/10.1021/ct400341pDOI Listing
July 2013

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters.

J Chem Theory Comput 2013 May;9(5):2339-2354

Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 771 46, Olomouc, Czech Republic.

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http://pubs.acs.org/doi/10.1021/ct400154j
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http://dx.doi.org/10.1021/ct400154jDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3775469PMC
May 2013

Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations.

J Phys Chem B 2013 Apr 4;117(15):4014-27. Epub 2013 Apr 4.

Department of Medicinal Chemistry, College of Pharmacy, 2000 East 30 South Skaggs 201, University of Utah, Salt Lake City, Utah 84112, USA.

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http://dx.doi.org/10.1021/jp400530eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3775460PMC
April 2013

iBIOMES: managing and sharing biomolecular simulation data in a distributed environment.

J Chem Inf Model 2013 Mar 5;53(3):726-36. Epub 2013 Mar 5.

Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah, United States.

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http://pubs.acs.org/doi/10.1021/ci300524j
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http://dx.doi.org/10.1021/ci300524jDOI Listing
March 2013

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.

Biochim Biophys Acta 2012 Oct 4;1820(10):1605-17. Epub 2012 Jun 4.

Department of Pharmacology and Toxicology, College of Pharmacy, Skaggs Hall 201, University of Utah, Salt Lake City, UT 84112, USA.

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http://dx.doi.org/10.1016/j.bbagen.2012.05.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3404218PMC
October 2012

Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure.

J Biomol NMR 2012 Aug 20;53(4):321-39. Epub 2012 Jun 20.

Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 201, Salt Lake City, UT 84112, USA.

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http://dx.doi.org/10.1007/s10858-012-9642-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3405240PMC
August 2012

The ABCs of molecular dynamics simulations on B-DNA, circa 2012.

J Biosci 2012 Jul;37(3):379-97

Department of Chemistry and Molecular Biophysics Program, Wesleyan University Middletown, CT 06459, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029509PMC
http://dx.doi.org/10.1007/s12038-012-9222-6DOI Listing
July 2012

Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.

J Chem Theory Comput 2012 Jul 5;8(7):2506-2520. Epub 2012 Jun 5.

Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic.

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http://dx.doi.org/10.1021/ct300275sDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3506181PMC
July 2012

Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures.

Methods 2012 May 16;57(1):25-39. Epub 2012 Apr 16.

Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic.

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http://dx.doi.org/10.1016/j.ymeth.2012.04.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3775459PMC
May 2012

Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle.

J Comput Chem 2012 Jan 14;33(2):119-33. Epub 2011 Oct 14.

Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, Utah 84112, USA.

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http://doi.wiley.com/10.1002/jcc.21922
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http://dx.doi.org/10.1002/jcc.21922DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242737PMC
January 2012

Improved coiled-coil design enhances interaction with Bcr-Abl and induces apoptosis.

Mol Pharm 2012 01 12;9(1):187-95. Epub 2011 Dec 12.

Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah 84108, United States.

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http://dx.doi.org/10.1021/mp200461sDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3313827PMC
January 2012

Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis.

J Am Chem Soc 2011 Sep 19;133(36):14270-9. Epub 2011 Aug 19.

Department of Medicinal Chemistry, College of Pharmacy, Skaggs Hall 201, University of Utah, Salt Lake City, Utah 84112, USA.

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http://dx.doi.org/10.1021/ja107805rDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3168932PMC
September 2011

Disruption of Bcr-Abl coiled coil oligomerization by design.

J Biol Chem 2011 Aug 9;286(31):27751-60. Epub 2011 Jun 9.

Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah 84108, USA.

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http://dx.doi.org/10.1074/jbc.M111.264903DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149365PMC
August 2011

Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes.

Nucleic Acids Res 2011 May 3;39(10):4499-512. Epub 2011 Feb 3.

Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkr031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105399PMC
May 2011

A coarse-grained model of DNA with explicit solvation by water and ions.

J Phys Chem B 2011 Jan 14;115(1):132-42. Epub 2010 Dec 14.

Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3019136PMC
January 2011

Improved cytochrome P450 3A4 molecular models accurately predict the Phe215 requirement for raloxifene dehydrogenation selectivity.

Biochemistry 2010 Oct;49(41):9011-9

Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA.

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http://dx.doi.org/10.1021/bi101139qDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2958526PMC
October 2010

Inhibitor-induced structural change in the HCV IRES domain IIa RNA.

Proc Natl Acad Sci U S A 2010 Apr 1;107(16):7263-8. Epub 2010 Apr 1.

Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA.

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http://dx.doi.org/10.1073/pnas.0911896107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2867761PMC
April 2010

Explicitly solvated ligand contribution to continuum solvation models for binding free energies: selectivity of theophylline binding to an RNA aptamer.

J Phys Chem B 2010 Feb;114(6):2227-37

Department of Experimental Oncology, Room 3336, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB, Canada.

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http://dx.doi.org/10.1021/jp9059664DOI Listing
February 2010

Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters.

J Phys Chem B 2009 Oct;113(40):13279-90

Department of Bioengineering, College of Engineering, Department of Medicinal Chemistry, College of Pharmacy, and Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, USA.

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http://dx.doi.org/10.1021/jp902584cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755304PMC
October 2009

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields.

J Chem Theory Comput 2009 Sep 19;5(9):2514-30. Epub 2009 Aug 19.

National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain, Department of Biochemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Spain, and Departments of Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 30 South 2000 East, Salt Lake City, Utah 84112.

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http://dx.doi.org/10.1021/ct900200kDOI Listing
September 2009

Molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coils.

Proteins 2009 Feb;74(3):612-29

Department of Pharmaceutics, University of Utah, Salt Lake City, Utah 84112, USA.

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http://dx.doi.org/10.1002/prot.22177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2692595PMC
February 2009

Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids.

J Phys Chem B 2008 Jul 18;112(27):8188-97. Epub 2008 Jun 18.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo namesti 2, 166 10, Prague 6, Czech Republic.

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http://dx.doi.org/10.1021/jp801245hDOI Listing
July 2008

Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations.

J Phys Chem B 2008 Jul 2;112(30):9020-41. Epub 2008 Jul 2.

Department of Bioengineering, College of Engineering, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112, USA.

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http://dx.doi.org/10.1021/jp8001614DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2652252PMC
July 2008

Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms.

J Chem Theory Comput 2007 Nov;3(6):2312-34

Departments of Medicinal Chemistry, Pharmaceutics and Pharmaceutical Chemistry, and Bioengineering, College of Pharmacy, University of Utah, 2000 East 30 South, Skaggs Hall 201, Salt Lake City, Utah 84112.

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http://pubs.acs.org/doi/abs/10.1021/ct700119m
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November 2007

Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue?

J Chem Theory Comput 2007 Sep;3(5):1851-9

Architecture et Réactivité de l'ARN, Université Louis Pasteur de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France, and Department of Medical Chemistry, Pharmaceutical Chemistry and Pharmaceutics and Bioengineering, University of Utah, Salt Lake City, Utah 84112.

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http://pubs.acs.org/doi/abs/10.1021/ct700143s
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September 2007

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.

Biophys J 2007 Jun 9;92(11):3817-29. Epub 2007 Mar 9.

Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica & Instituto Nacional de Bioinformática, Parc Científic de Barcelona, Barcelona 08028, Spain.

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http://dx.doi.org/10.1529/biophysj.106.097782DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868997PMC
June 2007

An accurate and simple quantum model for liquid water.

J Chem Phys 2006 Nov;125(18):184507

Center for Biophysical Modeling and Simulation, University of Utah, Salt Lake City, Utah 84112, USA.

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http://dx.doi.org/10.1063/1.2386157DOI Listing
November 2006

Computational Science and Engineering Online (CSE-Online): a cyber-infrastructure for scientific computing.

J Chem Inf Model 2006 May-Jun;46(3):971-84

Department of Chemistry and the Interdisciplinary Computational, Engineering, and Science Program, Department of Medicinal Chemistry, University of Utah, 315 South 1400 East, Rm 2020, Salt Lake City, Utah 84112, USA.

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http://dx.doi.org/10.1021/ci0503917DOI Listing
June 2006

The Amber biomolecular simulation programs.

J Comput Chem 2005 Dec;26(16):1668-88

Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1002/jcc.20290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1989667PMC
December 2005

Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations.

Biophys J 2004 Jul;87(1):227-42

National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic.

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http://dx.doi.org/10.1529/biophysj.103.034751DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304345PMC
July 2004

Simulation and modeling of nucleic acid structure, dynamics and interactions.

Curr Opin Struct Biol 2004 Jun;14(3):360-7

Department of Medicinal Chemistry, University of Utah, 2000 East, 30 South, Skaggs Hall 201, Salt Lake City, Utah 84112, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S0959440X0400075
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http://dx.doi.org/10.1016/j.sbi.2004.05.001DOI Listing
June 2004

DNA deformability at the base pair level.

J Am Chem Soc 2004 Apr;126(13):4124-5

Division Biophysics of Macromolecules, German Cancer Research Centre (DKFZ), 69120 Heidelberg, Germany.

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http://dx.doi.org/10.1021/ja0390449DOI Listing
April 2004

DNA basepair step deformability inferred from molecular dynamics simulations.

Biophys J 2003 Nov;85(5):2872-83

German Cancer Research Centre, 69120 Heidelberg, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1303568PMC
http://dx.doi.org/10.1016/S0006-3495(03)74710-9DOI Listing
November 2003

Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and DNA duplexes in solution.

J Am Chem Soc 2003 Feb;125(7):1759-69

Institute of Biophysics, Academy of Sciences of the Czech Republic, and National Center for Biomolecular Research, Královopolská 135, 612 65 Brno, Czech Republic.

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http://dx.doi.org/10.1021/ja025660dDOI Listing
February 2003

Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts.

Biophys J 2002 May;82(5):2592-609

J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, and Center for Complex Molecular Systems and Biomolecules, 182 23 Praha 8, Czech Republic.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1302048PMC
http://dx.doi.org/10.1016/s0006-3495(02)75601-4DOI Listing
May 2002