Thomas Cheatham

University of Utah

Chemistry

2016

Galindo-Murillo, Rodrigo and Robertson, James C. and Zgarbová, Marie and Šponer, Jiří and Otyepka, Michal and Jurečka, Petr and Cheatham, Thomas E. (2016): Assessing the Current State of Amber Force Field Modifications for DNA, Journal of Chemical Theory and Computation, American Chemical Society (ACS), Vol 12, Num 8, pp4114-4127
Christina Bergonzo, Kathleen B. Hall, and Thomas E. Cheatham (2016): Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics, J. Chem. Theory Comput., American Chemical Society (ACS), Vol 12, Num 7, pp3382--3389
James T. Waters, Xiang-Jun Lu, Rodrigo Galindo-Murillo, James C. Gumbart, Harold D. Kim, Thomas E. Cheatham, and Stephen C. Harvey (2016): Transitions of Double-Stranded DNA Between the A- and B-Forms, The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 120, Num 33, pp8449-8456
Lucía Álvarez, Ariel Lewis-Ballester, Adrián Roitberg, Darío A. Estrin, Syun-Ru Yeh, Marcelo A. Marti, and Luciana Capece (2016): Structural Study of a Flexible Active Site Loop in Human Indoleamine 2, 3-Dioxygenase and Its Functional Implications, Biochemistry, American Chemical Society (ACS), Vol 55, Num 19, pp2785--2793
Rodrigo Galindo-Murillo, Darrell R. Davis, and Thomas E. Cheatham (2016): Probing the Influence of Hypermodified Residues Within the tRNA3Lys Anticodon Stem Loop Interacting with the A-Loop Primer Sequence from HIV-1, Biochimica et Biophysica Acta (BBA) - General Subjects, Elsevier BV, Vol 1860, Num 3, pp607--617

2015

George M. Giambaşu, Darrin M. York, and David A. Case (2015): Structural Fidelity and NMR Relaxation Analysis in a Prototype RNA Hairpin, RNA, Cold Spring Harbor Laboratory Press, Vol 21, Num 5, pp963--974
Hai Nguyen, Alberto Pérez, Sherry Bermeo, and Carlos Simmerling (2015): Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins, Journal of Chemical Theory and Computation, American Chemical Society (ACS), Vol 11, Num 8, pp3714--3728
Rodrigo Galindo-Murillo, Daniel R. Roe, and Thomas E. Cheatham (2015): Convergence and Reproducibility in Molecular Dynamics Simulations of the DNA Duplex d(GCACGAACGAACGAACGC), Biochimica et Biophysica Acta (BBA) - General Subjects, Elsevier BV, Vol 1850, Num 5, pp1041--1058
Chad W. Hopkins, Scott Le Grand, Ross C. Walker, and Adrian E. Roitberg (2015): Long-Time-Step Molecular Dynamics Through Hydrogen Mass Repartitioning, J. Chem. Theory Comput., American Chemical Society (ACS), Vol 11, Num 4, pp1864--1874
Cheng-Tsung Lai, Huei-Jiun Li, Weixuan Yu, Sonam Shah, Gopal R. Bommineni, Victoria Perrone, Miguel Garcia-Diaz, Peter J. Tonge, and Carlos Simmerling (2015): Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium Tuberculosis InhA, Biochemistry, American Chemical Society (ACS), Vol 54, Num 30, pp4683--4691
Christina Bergonzo, and Thomas E. Cheatham (2015): Improved Force Field Parameters Lead to a Better Description of RNA Structure, J. Chem. Theory Comput., American Chemical Society (ACS), Vol 11, Num 9, pp3969--3972
Christina Bergonzo, Kathleen B. Hall, and Thomas E. Cheatham (2015): 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, American Chemical Society (ACS), Vol 119, Num 38, pp12355--12364
Christina Bergonzo, Niel M. Henriksen, Daniel R. Roe, and Thomas E. Cheatham (2015): Highly Sampled Tetranucleotide and Tetraloop Motifs Enable Evaluation of Common RNA Force Fields, RNA, Cold Spring Harbor Laboratory Press, Vol 21, Num 9, pp1578--1590
James A. Maier, Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin E. Hauser, and Carlos Simmerling (2015): ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB, J. Chem. Theory Comput., American Chemical Society (ACS), Vol 11, Num 8, pp3696--3713
James C. Robertson, and Thomas E Cheatham (2015): DNA Backbone BI/BII Distribution and Dynamics in E2 Protein-Bound Environment Determined by Molecular Dynamics Simulations, The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 119, Num 44, pp14111--14119
R. Galindo-Murillo, J. C. Garcia-Ramos, L. Ruiz-Azuara, T. E. Cheatham, and F. Cortes-Guzman (2015): Intercalation Processes of Copper Complexes in DNA, Nucleic Acids Research, Oxford University Press (OUP), Vol 43, Num 11, pp5364--5376
Thakshila Dissanayake, Jason M. Swails, Michael E. Harris, Adrian E. Roitberg, and Darrin M. York (2015): Interpretation of pH-Activity Profiles for Acid-Base Catalysis from Molecular Simulations, Biochemistry, American Chemical Society (ACS), Vol 54, Num 6, pp1307--1313
Thomas E. Cheatham, and Daniel R. Roe (2015): The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis, Comput. Sci. Eng., Institute of Electrical & Electronics Engineers (IEEE), Vol 17, Num 2, pp30--39

2014

Christina Bergonzo, Niel M. Henriksen, Daniel R. Roe, Jason M. Swails, Adrian E. Roitberg, and Thomas E. Cheatham (2014): Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide, J. Chem. Theory Comput., American Chemical Society (ACS), Vol 10, Num 1, pp492--499
Daniel R. Roe, Christina Bergonzo, and Thomas E. Cheatham (2014): Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics With Hamiltonian Replica Exchange Methods, The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 118, Num 13, pp3543--3552
Rodrigo Galindo-Murillo, Daniel R. Roe, and Thomas E. Cheatham (2014): On the absence of intrahelical DNA dynamics on the μs to ms timescale, Nature Communications, Nature Publishing Group, Vol 5, pp5152
Hai Nguyen, James Maier, He Huang, Victoria Perrone, and Carlos Simmerling (2014): Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent, J. Am. Chem. Soc., American Chemical Society (ACS), Vol 136, Num 40, pp13959--13962
Jason M. Swails, Darrin M. York, and Adrian E. Roitberg (2014): Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation, J. Chem. Theory Comput., American Chemical Society (ACS), Vol 10, Num 3, pp1341--1352
Julien C Thibault, Daniel R Roe, Julio C Facelli, and Thomas E Cheatham (2014): Data Model, Dictionaries, and Desiderata for Biomolecular Simulation Data Indexing and Sharing, Journal of Cheminformatics, Springer Nature, Vol 6, Num 1, pp4
Julien C. Thibault, Thomas E. Cheatham, and Julio C. Facelli (2014): iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings, Journal of Chemical Information and Modeling, American Chemical Society (ACS), Vol 54, Num 6, pp1810--1819
Natali V. Di Russo, Marcelo A. Marti, and Adrian E. Roitberg (2014): Underlying Thermodynamics of pH-Dependent Allostery, The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 118, Num 45, pp12818--12826
Niel M. Henriksen, Hamed S. Hayatshahi, Darrell R. Davis, and Thomas E. Cheatham (2014): 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, American Chemical Society (ACS), Vol 54, Num 6, pp1758--1772
T. Dwight McGee, Jesse Edwards, and Adrian E. Roitberg (2014): pH-REMD Simulations Indicate That the Catalytic Aspartates of HIV-1 Protease Exist Primarily in a Monoprotonated State, The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 118, Num 44, pp12577--12585

2013

Daniel R. Roe, and Thomas E. Cheatham (2013): PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data, J. Chem. Theory Comput., American Chemical Society (ACS), Vol 9, Num 7, pp3084--3095

2015 Blue Waters Symposium highlights successes, looks to the future of supercomputing

The 2015 Blue Waters Symposium, held May 10-13 at Oregon's beautiful Sunriver Resort, brought together leaders in petascale computational science and engineering to share successes and methods. Around 130 attendees, many of whom were Blue Waters users and the NCSA staff who support their work, enjoyed presentations on computational advances in a range of research areas—including sub-atomic physics, weather, biology, astronomy, and many others—as well as keynotes from innovative thinkers and leaders in high-performance computing. Over the three days of the symposium, 58 science teams from across the country presented on their work on Blue Waters..

NSF awards time on Blue Waters to seven new projects

The National Science Foundation (NSF) has awarded 14 new allocations on the Blue Waters petascale supercomputer at the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign. Seven of the awards are for new projects..

Blue Waters to help researchers tackle Ebola

NCSA’s Blue Waters supercomputer will be used by three research teams to gain new understanding of the deadly Ebola virus, thanks to allocations provided through the National Science Foundation’s Rapid Response Research program. “As the nation’s most powerful and productive supercomputer for open science, Blue Waters plays a vital role in a wide range of research that impacts our lives,” said Blue Waters leader Bill Kramer. “Blue Waters is helping scientists better understand Alzheimer’s disease, HIV, earthquakes, and dangerous tornadoes, and we’re gratified that now we can help address the global threat of Ebola.”.

Fixing and flexing biomolecular force fields

A University of Utah research group is using the massive scale of Blue Waters to rapidly and rigorously evaluate the force fields used in molecular dynamics simulations.Thomas Cheatham’s University of Utah research team uses molecular dynamics simulations to better understand biomolecules, like nucleic acids and proteins. Improving and validating their methods, and the Amber tools and force fields that they use, is a critical part of that work.“You can model anything; that doesn’t mean it’s real,” points out Cheatham, an associate professor of medicinal chemistry. “We constantly have to assess and validate results with comparison to experiment.”.