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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DNA repair enzymes ALKBH2, ALKBH3, and AlkB oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine in vitro.
Ke Bian,Stefan A. P. Lenz,Qi Tang,Fangyi Chen,Rui Qi,Marco Jost,Catherine L. Drennan,John M. Essigmann,Stacey D. Wetmore,Deyu Li +9 more
TL;DR: This is the first demonstration of the AlkB proteins to oxidize a methyl group attached to carbon, instead of nitrogen, on a DNA base, which suggests a broader role in epigenetics for these DNA repair proteins.
Journal ArticleDOI
Engineering couplings for exciton transport using synthetic DNA scaffolds
Stephanie M. Hart,Wei Jia Chen,James L. Banal,William P. Bricker,William P. Bricker,Amro Dodin,Larysa I. Markova,Yuliia Vyborna,Adam P. Willard,Robert Häner,Mark Bathe,Gabriela S. Schlau-Cohen +11 more
TL;DR: It is demonstrated that the coupling between the chromophores and the environment could enhance exciton transport efficiency, highlighting the key role of the environment in driving exciton dynamics.
Journal ArticleDOI
Conformational dynamics is key to understanding loss-of-function of NQO1 cancer-associated polymorphisms and its correction by pharmacological ligands
Encarnación Medina-Carmona,Rogelio Palomino-Morales,Julian E. Fuchs,Esperanza Padín-González,Noel Mesa-Torres,Eduardo Salido,David J. Timson,Angel L. Pey +7 more
TL;DR: Protein dynamics are fundamental to understanding loss-of-function in p.P187S, and to develop new pharmacological therapies to rescue this function, and a directional preference in NQO1 proteasomal degradation and the use of ligands binding to this domain to stabilize p.
Journal ArticleDOI
Improving the thermostability and catalytic efficiency of glucose oxidase from Aspergillus niger by molecular evolution.
TL;DR: Key properties of glucose oxidase can be modified in vitro by laboratory evolution, which may have remarkable economic importance as well as enhance thermostability and catalytic efficiency.
Journal ArticleDOI
Molecular mechanism with regard to the binding selectivity of inhibitors toward FABP5 and FABP7 explored by multiple short molecular dynamics simulations and free energy analyses.
TL;DR: Binding free energies predicted by the molecular mechanics/generalized Born surface area (MM-GBSA) method indicate that the increase in the enthalpy changes caused by the bindings of inhibitors toward FABP7 relative to FAB p5 mostly drives the binding selectivity of the inhibitors towardFABP5 versus FABp7.
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.
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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
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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.