Thomas Cheatham
COVID-19 main protease inhibitor design
(bbcm)Apr 2020 - Jun 2020
Ensembles of molecular dynamics engines for assessing force fields, conformational change, and free energies of proteins and nucleic acids
(gk4)Aug 2017 - Jul 2018
PAID-MD Trajectory Perf. Optimization
(gkl)Sep 2015 - Aug 2016
2020
Ankita Sarkar and Adrian E. Roitberg (2020): pH-Dependent Conformational Changes Lead to a Highly Shifted pKa for a Buried Glutamic Acid Mutant of SNase, Journal of Physical Chemistry B, American Chemical Society, Vol 124, Num 49, pp11072-11080
Abir Ganguly, Benjamin P. Weissman, Timothy J. Giese, Nan-Sheng Li, Shuichi Hoshika, Saieesh Rao, Steven A. Benner, Joseph A. Piccirilli, and Darrin M. York (2020): Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme, Nature Chemistry, Springer Nature Limited, Vol 12, Num 2, pp193–201
2019
Rodrigo Galindo-Murillo, Thomas E. Cheatham, and Robert C. Hopkins (2019): Exploring Potentially Alternative Non-Canonical DNA Duplex Structures Through Simulation, Journal of Biomolecular Structure and Dynamics, Taylor & Francis, Vol 37, Num 9, pp2201-2210
Colin S. Gaines, Timothy J. Giese, and Darrin M. York (2019): Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology, ACS Catalysis, Vol 9, Num 7, pp5803-5815
Vinicius Wilian D. Cruzeiro and Adrian E. Roitberg (2019): Multidimensional Replica Exchange Simulations for Efficient Constant pH and Redox Potential Molecular Dynamics, Journal of Chemical Theory and Computation, American Chemical Society, Vol 15, Num 2, pp871-881
Ankita Sarkar, Pancham Lal Gupta, and Adrian E. Roitberg (2019): pH-Dependent Conformational Changes Due to Ionizable Residues in a Hydrophobic Protein Interior: The Study of L25K and L125K Variants of SNase, Journal of Physical Chemistry B, American Chemical Society, Vol 123, Num 27, pp5742-5754
2018
Sean P. Cornillie, Benjamin J. Bruno, Carol S. Lim, and Thomas E. Cheatham (2018): Computational Modeling of Stapled Peptides Toward a Treatment Strategy for CML and Broader Implications in the Design of Lengthy Peptide Therapeutics, Journal of Physical Chemistry B, American Chemical Society, Vol 122, Num 14, pp3864-3875
Daniel R. Roe and Thomas E. Cheatham (2018): Parallelization of CPPTRAJ Enables Large Scale Analysis of Molecular Dynamics Trajectory Data, Journal of Computational Chemistry, Wiley, Vol 39, Num 25, pp2110-2117
Vinícius Wilian D. Cruzeiro, and Marcos S. Amaral, and Adrian E. Roitberg (2018): Redox potential replica exchange molecular dynamics at constant pH in AMBER: Implementation and validation, Journal of Chemical Physics, AIP Publishing LLC, Vol 149, Num 7, pp072338
He Huang and Carlos Simmerling (2018): Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs, Journal of Chemical Theory and Computation, American Chemical Society, Vol 14, Num 11, pp5797-5814
Tai-Sung Lee, David S. Cerutti, Dan Mermelstein, Charles Lin, Scott LeGrand, Timothy J. Giese, Adrian Roitberg. David A. Case, Ross C. Walker, and Darrin M. York (2018): GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features, Journal of Chemical Information and Modeling, American Chemical Society, Vol 58, Num 10, pp2043-2050
2017
Juan I. Blanco Capurro, Chad W. Hopkins, Gustavo Pierdominici Sottile, Mariano C. González Lebrero, Adrian E. Roitberg, and Marcelo A. Marti (2017): Theoretical Insights Into the Reaction and Inhibition Mechanism of Metal-Independent Retaining Glycosyltransferase Responsible for Mycothiol Biosynthesis, Journal of Physical Chemistry B, American Chemical Society, Vol 121, Num 3, pp471-478
Christina Bergonzo and Thomas E. Cheatham (2017): Mg2+ Binding Promotes SLV as a Scaffold in Varkud Satellite Ribozyme SLI-SLV Kissing Loop Junction, Biophysical Journal, Elsevier BV, Vol 113, Num 2, pp313-320
Kevin Hauser, Yiqing He, Miguel Garcia-Diaz, Carlos Simmerling, and Evangelos Coutsias (2017): Characterization of Biomolecular Helices and Their Complementarity Using Geometric Analysis, Journal of Chemical Information and Modeling, American Chemical Society, Vol 57, Num 4, pp864-874
Haoquan Li, Anton V. Endutkin, Christina Bergonzo, Lin Fu, Arthur Grollman, Dmitry O. Zharkov, and Carlos Simmerling (2017): DNA Deformation-Coupled Recognition of 8-Oxoguanine: Conformational Kinetic Gating in Human DNA Glycosylase, Journal of the American Chemical Society, American Chemical Society, Vol 139, Num 7, pp2682-2692
2016
Claudia L. Ramírez, Ariel Petruk, Mauro Bringas, Dario A. Estrin, Adrian E. Roitberg, Marcelo A. Marti, and Luciana Capece (2016): Coarse-Grained Simulations of Heme Proteins: Validation and Study of Large Conformational Transitions, Journal of Chemical Theory and Computation, American Chemical Society, Vol 12, Num 7, pp3390-3397
Raúl Esteban Ithuralde, Adrián Enrique Roitberg, and Adrián Gustavo Turjanski (2016): Structured and Unstructured Binding of an Intrinsically Disordered Protein as Revealed by Atomistic Simulations, Journal of the American Chemical Society, American Chemical Society, Vol 138, Num 28, pp8742-8751
Zahra Heidari, Daniel R. Roe, Rodrigo Galindo-Murillo, Jahan B. Ghasemi, and Thomas E. Cheatham (2016): Using Wavelet Analysis to Assist in Identification of Significant Events in Molecular Dynamics Simulations, Journal of Chemical Information and Modeling, American Chemical Society, Vol 56, Num 7, pp1282-1291
Hauser, Kevin and Essuman, Bernard and He, Yiqing and Coutsias, Evangelos and Garcia-Diaz, Miguel, and Simmerling, Carlos (2016): A human transcription factor in search mode, Nucleic Acids Research, Oxford University Press, Vol 44, Num 1, pp63-74
Rodrigo Galindo-Murillo and Thomas E. Cheatham (2016): Computational DNA Binding Studies of (-)-Epigallocatechin-3-Gallate, Journal of Biomolecular Structure and Dynamics, Informa UK Limited, Vol 113, Num 49, pp1-13
Christina Bergonzo, Kathleen B. Hall, and Thomas E. Cheatham (2016): Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics, Journal of Chemical Theory and Computation, American Chemical Society, 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, Journal of Physical Chemistry B, American Chemical Society, 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, 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
Rodrigo Galindo-Murillo, James C. Robertson, Marie Zgarbová, Jiří Šponer, Michal Otyepka, Petr Jurečka, and Thomas E. Cheatham III (2016): Assessing the Current State of Amber Force Field Modifications for DNA, Journal of Chemical Theory and Computation, American Chemical Society, Vol 12, Num 8, pp4114-4127
2015
Maria T. Panteva, Thakshila Dissanayake, Haoyuan Chen, Brian K. Radak, Erich R. Kuechler, George M. Giambaşu, Tai-Sung Lee, and Darrin M. York (2015): Multiscale Methods for Computational RNA Enzymology, Elsevier, Methods in Enzymology, pp335-374
Brian K. Radak, Tai-Sung Lee, Michael E. Harris, and Darrin M. York (2015): Assessment of Metal-Assisted Nucleophile Activation in the Hepatitis Delta Virus Ribozyme from Molecular Simulation and 3D-RISM, RNA, Cold Spring Harbor Laboratory, Vol 21, Num 9, pp1566-1577
Maria T. Panteva, George M. Giambaşu, and Darrin M. York (2015): Comparison of Structural, Thermodynamic, Kinetic and Mass Transport Properties of Mg2+ion Models Commonly Used in Biomolecular Simulations, Journal of Computational Chemistry, Wiley, Vol 36, Num 13, pp970-982
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, Journal of Chemical Theory and Computation, American Chemical Society, 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, 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, Journal of Chemical Theory and Computation, American Chemical Society, 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, Journal of Physical Chemistry B, American Chemical Society, 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
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, Vol 11, Num 8, pp3714-3728
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, Journal of Chemical Theory and Computation, American Chemical Society, 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, Journal of Physical Chemistry B, American Chemical Society, 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, 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, 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, Computing in Science & Engineering, Institute of Electrical & Electronics Engineers, Vol 17, Num 2, pp30-39
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
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, Journal of Chemical Theory and Computation, American Chemical Society, 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, Journal of Physical Chemistry B, American Chemical Society, 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 mu s 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, Journal of the American Chemical Society, American Chemical Society, 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, Journal of Chemical Theory and Computation, American Chemical Society, 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, Vol 54, Num 6, pp1810-1819
Natali V. Di Russo, Marcelo A. Marti, and Adrian E. Roitberg (2014): Underlying Thermodynamics of pH-Dependent Allostery, Journal of Physical Chemistry B, American Chemical Society, Vol 118, Num 45, pp12818-12826
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, Journal of Physical Chemistry B, American Chemical Society, Vol 118, Num 44, pp12577-12585
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, Vol 54, Num 6, pp1758-1772
2013
Daniel R. Roe and Thomas E. Cheatham (2013): PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data, Journal of Chemical Theory and Computation, American Chemical Society, Vol 9, Num 7, pp3084-3095
2019
Victor Anisimov, Valery Poltev, Thomas E. Cheatham III, Jerry Bernholc, Rodrigo Galindo–Nurillo (2019): Improving the Agreement of AMBER Simulation of Crystals of Nucleic Acid Bases with Experimental Data, 2019 Blue Waters Annual Report, pp314-315
2018
Thomas Cheatham, Adrian Roitberg, Carlos Simmerling, David Case, Darrin York, Rodrigo Galindo Murillo, Daniel Roe, Christina Bergonzo, Niel Henriksen, Hamed Hayatshahi (2018): Using Large Ensembles of AMBER Molecular Dynamics Simulations to Reproducibly and Reliably Converge the Conformational Distributions of Nucleic Acids, 2018 Blue Waters Annual Report, pp212-215
2017
Thomas Cheatham (2017): Exploring The Structure and Dynamics of Converged Ensembles of DNA and RNA through Molecular Dynamics Simulations, 2017 Blue Waters Annual Report, pp204-205
2016
Thomas Cheatham (2016): Understanding Biomolecular Structure and Dynamics by Overcoming Barriers to Conformational Sampling, 2016 Blue Waters Annual Report, pp203-205
2015
Thomas Cheatham (2015): Convergence and Reproducibility in Simulations of Nucleic Acids, 2015 Blue Waters Annual Report, pp132-133
Thomas Cheatham: Reproducibility, Convergence and Accuracy in Biomolecular Simulation of Nucleic Acids Conformational Ensembles
Blue Waters Symposium 2019, Jun 5, 2019
Thomas Cheatham: Using Ensembles of Molecular Dynamics Simulations to Give Insight into Biomolecular Structure, Dynamics and Function
Blue Waters Symposium 2018, Jun 6, 2018
Thomas Cheatham: AMBER Biomolecular Dynamics Simulations Provide Novel Insight into Nucleic Acid Structure, Dynamics and Function
Blue Waters Symposium 2017, May 18, 2017
Thomas Cheatham: Ensembles of MD Simulations to Assess, Validate, Improve, and Enable Force Fields for Exploring RNA Structure and Dynamics
Blue Waters Symposium 2016, Jun 13, 2016
Thomas Cheatham: Convergence and reproducibility in molecular dynamics simulations of nucleic acids enabled by Blue Waters
Blue Waters Symposium 2015, May 11, 2015
Thomas Cheatham: Hierarchical molecular dynamics sampling for assessing pathways and free energies of RNA catalysis, ligand binding, and conformational change
Blue Waters Symposium 2014, May 13, 2014
Gold standard force fields help identify promising peptides to disrupt COVID-19
Apr 28, 2020
Thomas Cheatham—a professor of medicinal chemistry and director of the Center for High Performance Computing at the University of Utah—and Rodrigo Galindo—a research professor in his group—use powerful supercomputers to predict the characteristics of novel drugs.
Sources:
- https://phys.org/news/2020-04-gold-standard-fields-peptides-disrupt.html
- https://www.news-medical.net/news/20200430/Scientists-generate-molecular-models-of-compounds-relevant-for-COVID-19.aspx
- https://www.techrepublic.com/article/supercomputers-playing-a-significant-role-in-covid-19-research/
- http://www.bio-itworld.com/2020/05/01/data-kits-supercomputers-and-llamas-bio-it-community-leaves-no-stone-unturned-in-covid-19-research.aspx
- https://www.eurekalert.org/pub_releases/2020-04/uota-gsf042820.php
2015 Blue Waters Symposium highlights successes, looks to the future of supercomputing
May 29, 2015
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.
Sources:
Blue Waters to help researchers tackle Ebola
Apr 7, 2015
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.”
Sources:
NSF awards time on Blue Waters to seven new projects
Oct 1, 2014
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.
Sources:
Fixing and flexing biomolecular force fields
Mar 20, 2014
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.”
Sources:
