Journal ArticleDOI
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe,Thomas E. Cheatham +1 more
Reads0
Chats0
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
More filters
Journal ArticleDOI
Integrating protein structural dynamics and evolutionary analysis with Bio3D
TL;DR: The integration of structural dynamics and evolutionary analysis in Bio3D enables researchers to go beyond a prediction of single protein dynamics to investigate dynamical features across large protein families.
Journal ArticleDOI
Modeling and Simulations of Polymers: A Roadmap
TL;DR: In this article, the authors discuss their philosophy for carefully developing or selecting appropriate models, performing, and analyzing polymer simulations, highlighting best practices, key challenges, and important advances in model development/selection, computational method choices, advanced sampling met...
Journal ArticleDOI
Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data.
Abbas Khan,Tauqir Zia,Muhammad Suleman,Taimoor Khan,Syed Shujait Ali,Aamir Ali Abbasi,Anwar Mohammad,Dong-Qing Wei +7 more
TL;DR: In this article, a structural and biophysical analysis of the Spike glycoprotein of SARS-CoV-2 new variants has been carried out to understand the binding and structural dynamics of the new mutations in the RBD domain of Spike protein.
Journal ArticleDOI
Crystal Structure of a Full-Length Human Tetraspanin Reveals a Cholesterol-Binding Pocket.
Brandon Zimmerman,Brendan Kelly,Brian J. McMillan,Tom C. M. Seegar,Ron O. Dror,Andrew C. Kruse,Stephen C. Blacklow,Stephen C. Blacklow +7 more
TL;DR: The crystal structure of human CD81 is reported, a full-length tetraspanin, and cholesterol binding appears to modulate CD81 activity in cells, suggesting a potential mechanism for regulation of tetrascanin function.
Journal ArticleDOI
Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15
Lee-Ping Wang,Keri A. McKiernan,Joseph Gomes,Kyle A. Beauchamp,Teresa Head-Gordon,Teresa Head-Gordon,Julia E. Rice,William C. Swope,Todd J. Martínez,Todd J. Martínez,Vijay S. Pande +10 more
TL;DR: The AMBER-FB15 protein force field was developed by building a high-quality quantum chemical data set consisting of comprehensive potential energy scans and employing the ForceBalance software package for parameter optimization, which allows for more significant thermodynamic fluctuations away from local minima.
References
More filters
Journal ArticleDOI
VMD: Visual molecular dynamics
TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.
Journal ArticleDOI
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
Wolfgang Kabsch,Chris Sander +1 more
TL;DR: A set of simple and physically motivated criteria for secondary structure, programmed as a pattern‐recognition process of hydrogen‐bonded and geometrical features extracted from x‐ray coordinates is developed.
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.
Journal ArticleDOI
CHARMM: the biomolecular simulation program.
Bernard R. Brooks,Charles L. Brooks,Alexander D. MacKerell,Lennart Nilsson,Robert J. Petrella,Benoît Roux,Youngdo Won,Georgios Archontis,Christian Bartels,Stefan Boresch,Amedeo Caflisch,Leo S. D. Caves,Qiang Cui,Aaron R. Dinner,Michael Feig,Stefan Fischer,Jiali Gao,Milan Hodošček,Wonpil Im,K. Kuczera,Themis Lazaridis,Jianpeng Ma,V. Ovchinnikov,Emanuele Paci,Richard W. Pastor,Carol Beth Post,Jingzhi Pu,M. Schaefer,Bruce Tidor,Richard M. Venable,H. L. Woodcock,Xiongwu Wu,Wei Yang,Darrin M. York,Martin Karplus,Martin Karplus +35 more
TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.
Journal ArticleDOI
General definition of ring puckering coordinates
Dieter Cremer,John A. Pople +1 more
TL;DR: In this article, a unique mean plane is defined for a general monocyclic puckered ring, which is described by amplitude and phase coordinates which are generalizations of those introduced for cyclopentane by Kilpatrick, Pitzer, and Spitzer.