Journal ArticleDOI
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe,Thomas E. Cheatham +1 more
TLDR
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.Abstract:
We describe PTRAJ and its successor CPPTRAJ, two complementary, portable, and freely available computer programs for the analysis and processing of time series of three-dimensional atomic positions (i.e., coordinate trajectories) and the data therein derived. Common tools include the ability to manipulate the data to convert among trajectory formats, process groups of trajectories generated with ensemble methods (e.g., replica exchange molecular dynamics), image with periodic boundary conditions, create average structures, strip subsets of the system, and perform calculations such as RMS fitting, measuring distances, B-factors, radii of gyration, radial distribution functions, and time correlations, among other actions and analyses. Both the PTRAJ and CPPTRAJ programs and source code are freely available under the GNU General Public License version 3 and are currently distributed within the AmberTools 12 suite of support programs that make up part of the Amber package of computer programs (see http://ambe...read more
Citations
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Journal ArticleDOI
Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics
TL;DR: Molecular dynamics simulations performed on a set of hairpin loops, duplexes and tetramers with the new parameter set show improved modeling for the structures of tetramer CCCC, CAAU, and GACC, and an RNA internal loop of noncanonical pairs, as compared to the conventional parameters.
Journal ArticleDOI
The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome
TL;DR: This work finds that the conformation adopted by the histone H3 tails is inhibitory to BPTF PHD finger binding, and alters the electrostatics of the H3 tail via modification or mutation, indicating that PTM crosstalk can regulate effector domain binding by altering nucleosome conformation.
Journal ArticleDOI
Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST
Steven Ramsey,Crystal N. Nguyen,Romelia Salomon-Ferrer,Ross C. Walker,Michael K. Gilson,Tom Kurtzman +5 more
TL;DR: Grid Inhomogeneous Solvation Theory (GIST) is incorporated into the CPPTRAJ toolset of AmberTools, and a set of open‐source tools are developed, called GISTPP, which facilitate the analysis of GIST output grids.
Journal ArticleDOI
Integrated Omics and Computational Glycobiology Reveal Structural Basis for Influenza A Virus Glycan Microheterogeneity and Host Interactions
Kshitij Khatri,Joshua A. Klein,Mitchell R. White,Oliver C. Grant,Nancy Leymarie,Robert J. Woods,Kevan L. Hartshorn,Joseph Zaia +7 more
TL;DR: A study that integrates proteomics, glycomics and glycoproteomics of HA before and after adaptation to innate immune system pressure to better define the relationships among glycosylation, viral bioactivity and evolution.
Journal ArticleDOI
Sampling alternative conformational states of transporters and receptors with AlphaFold2
TL;DR: In this article , an approach to drive AlphaFold2 to sample alternative conformations of topologically diverse transporters and G-protein-coupled receptors is presented.
References
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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
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