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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Journal ArticleDOI
Drug Binding Poses Relate Structure with Efficacy in the μ Opioid Receptor.
TL;DR: Investigation of ligand–residue interactions and receptor conformations in the μ-opioid receptor revealed that these ligands adopt distinct binding poses and engage different subsets of residues, despite sharing a common morphinan scaffold.
Journal ArticleDOI
Rational Redesign of Enzyme via the Combination of Quantum Mechanics/Molecular Mechanics, Molecular Dynamics, and Structural Biology Study.
Hong-Yan Lin,Xi Chen,Jin Dong,Jing-Fang Yang,Han Xiao,Ying Ye,Lin-Hui Li,Chang-Guo Zhan,Wen-Chao Yang,Guang-Fu Yang +9 more
TL;DR: In this paper, a rational redesign of a model enzyme, 4-hydroxyphenylpyruvate dioxygenase (HPPD), based on quantum mechanics/molecular mechanics (QM/MM) calculation and molecular dynamic simulations is reported.
Journal ArticleDOI
RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution.
Karolina M. Gorecka,Miroslav Krepl,Aleksandra Szlachcic,Jarosław Poznański,Jiří Šponer,Jiří Šponer,Marcin Nowotny +6 more
TL;DR: It is shown that correct positioning of the substrate for cleavage requires conformational changes within the bound DNA, which involve rare high-energy states with protein-assisted base flipping that are readily accessible for the cognate DNA sequence but not for non-cognate sequences.
Journal ArticleDOI
Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation.
D.R. Gruber,Joanna J Toner,H.L. Miears,Andrey V. Shernyukov,Alexey S. Kiryutin,Alexander A. Lomzov,Anton V. Endutkin,Inga R. Grin,Darya V. Petrova,Maxim S. Kupryushkin,Alexandra V. Yurkovskaya,Eric C Johnson,Mark Okon,Elena G. Bagryanskaya,Dmitry O. Zharkov,Serge L. Smirnov +15 more
TL;DR: It is shown that the presence of oxoG biases the recognition of methylated CpG dinucleotides by ROS1, a plant enzyme involved in epigenetic DNA demethylation, in favor of the oxidized DNA strand.
Journal ArticleDOI
Screening method for simultaneous detection of elaidic and vaccenic trans fatty acid isomers by capillary zone electrophoresis.
Tatiane Lima Amorim,Lucas Mattos Duarte,Hélio F. Dos Santos,Marcone Augusto Leal de Oliveira +3 more
TL;DR: The CZE-UV method proved to be simple, environmental friendly and sensitive and may be used to detect adulteration in dairy products, where the addition of hydrogenated vegetable fat to food is prohibited.
References
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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.
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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.