T
Thomas E. Cheatham
Researcher at University of Utah
Publications - 164
Citations - 38522
Thomas E. Cheatham is an academic researcher from University of Utah. The author has contributed to research in topics: Molecular dynamics & Nucleic acid. The author has an hindex of 58, co-authored 156 publications receiving 32976 citations. Previous affiliations of Thomas E. Cheatham include Free University of Berlin & University of California, San Francisco.
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Journal ArticleDOI
The Amber biomolecular simulation programs
David A. Case,Thomas E. Cheatham,Tom Darden,Holger Gohlke,Ray Luo,Kenneth M. Merz,Alexey V. Onufriev,Carlos Simmerling,Bing Wang,Robert J. Woods +9 more
TL;DR: The development, current features, and some directions for future development of the Amber package of computer programs, which contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.
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PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe,Thomas E. Cheatham +1 more
TL;DR: PTRAJ and its successor CPPTRAJ are described, two complementary, portable, and freely available computer programs for the analysis and processing of time series of three-dimensional atomic positions and the data therein derived.
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Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
Peter A. Kollman,Irina Massova,Carolina M. Reyes,Bernd Kuhn,Shuanghong Huo,Lillian T. Chong,Matthew Lee,Tai-Sung Lee,Yong Duan,Wei Wang,Oreola Donini,Piotr Cieplak,Jaysharee Srinivasan,David A. Case,Thomas E. Cheatham +14 more
TL;DR: A historical perspective on the application of molecular dynamics to biological macromolecules is presented and recent developments combining state-of-the-art force fields with continuum solvation calculations have allowed for the fourth era of MD applications in which one can often derive both accurate structure and accurate relative free energies from molecular dynamics trajectories.
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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
David A. Pearlman,David A. Case,James W. Caldwell,Wilson S. Ross,Thomas E. Cheatham,Steve DeBolt,David M. Ferguson,George Seibel,Peter A. Kollman +8 more
TL;DR: The development, current features, and some directions for future development of the AMBER package of computer programs are described, embodying a number of the powerful tools of modern computational chemistry-molecular dynamics and free energy calculations.
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Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations
InSuk Joung,Thomas E. Cheatham +1 more
TL;DR: These efforts to build better models of the monovalent ions within the pairwise Coulombic and 6-12 Lennard-Jones framework are described, where the models are tuned to balance crystal and solution properties in Ewald simulations with specific choices of well-known water models.