Journal ArticleDOI
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe,Thomas E. Cheatham +1 more
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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
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Dynamic Water-Mediated Hydrogen Bonding in a Collagen Model Peptide.
Iwen Fu,David A. Case,Jean Baum +2 more
TL;DR: Computational approaches with nuclear magnetic resonance (NMR) are integrated to obtain a dynamic view of hydrogen bonding distributions in the (POG)(4)(-)(POA)-( POG)(5) peptide, showing that the solution conformation, dynamics, and hydrogen bonding deviate from the reported X-ray crystal structure in many aspects.
Journal ArticleDOI
Multiple Pathways and Time Scales for Conformational Transitions in apo-Adenylate Kinase
Yuqing Zheng,Qiang Cui +1 more
TL;DR: No evidence is observed for any significant degree of local unfolding during the transition in apo AK, and the closed state ensemble is found to be kinetically heterogeneous; multiple pathways and time scales are associated with the open/close transition, providing new clues to the disparate time scales observed in different experiments.
Journal ArticleDOI
Distinct Substrate Transport Mechanism Identified in Homologous Sugar Transporters
TL;DR: This study provides biological insights on the unexplored novelty of difference in the functional mechanism of two close homologous proteins.
Journal ArticleDOI
Cryptic binding sites become accessible through surface reconstruction of the type I collagen fibril.
TL;DR: An early stage atomic model of the smallest repeating unit of the type I collagen fibrils at the fibril surface is developed that provides a novel framework to address questions about these functionally necessary yet seemingly obstructed interactions.
Journal ArticleDOI
Exploring Protein Stability by Comparative Molecular Dynamics Simulations of Homologous Hyperthermophilic, Mesophilic, and Psychrophilic Proteins.
TL;DR: The influence of temperature on the stability and dynamics of the α subunit of tryptophan synthase (TRPS) from hyperthermophilic, mesophilic and psychrophilic homologues at different temperatures by molecular dynamics simulations is analyzed.
References
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VMD: Visual molecular dynamics
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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.
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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.