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
Sharing Data from Molecular Simulations
Mark Abraham,Rossen Apostolov,Jonathan Barnoud,Paul Bauer,Christian Blau,Alexandre M. J. J. Bonvin,Matthieu Chavent,John D. Chodera,Karmen Condic-Jurkic,Lucie Delemotte,Helmut Grubmüller,Rebecca J. Howard,Rebecca J. Howard,E. Joseph Jordan,Erik Lindahl,Erik Lindahl,O. H. Samuli Ollila,Jana Selent,Daniel G. A. Smith,Phillip J. Stansfeld,Johanna K. S. Tiemann,Mikael Trellet,Christopher J. Woods,Artem Zhmurov +23 more
TL;DR: A brief overview of this workshop is presented, hoping this effort will spark further conversation in the MD community to pave the way towards more open, interoperable and reproducible outputs coming from research studies using MD simulations.
Journal ArticleDOI
Understanding the Mechanistic Requirements for Efficient and Stereoselective Alkene Epoxidation by a Cytochrome P450 Enzyme
T. Coleman,Alicia M. Kirk,Rebecca R. Chao,M.N. Podgorski,Joshua S. Harbort,Luke R. Churchman,John B. Bruning,Paul V. Bernhardt,Jeffrey Harmer,Elizabeth H. Krenske,James J. De Voss,Stephen Bell +11 more
TL;DR: The cytochrome P450 (CYP) family of heme monooxygenase enzymes commonly catalyzes enantioselective hydroxylation and epoxidation reactions.
Journal ArticleDOI
Viral engagement with host (co-)receptors blocked by a novel class of tryptophan dendrimers that targets the 5-fold-axis of the enterovirus-A71 capsid
Liang Sun,Hyunwook Lee,Hendrik Jan Thibaut,Kristina Lanko,Eva Rivero-Buceta,Carol M. Bator,Belén Martínez-Gualda,Kai Dallmeier,Leen Delang,Pieter Leyssen,Federico Gago,Ana San-Félix,Susan Hafenstein,Carmen Mirabelli,Johan Neyts +14 more
TL;DR: The binding region of MADAL385 is mapped to the 5-fold vertex of the viral capsid and it is demonstrated that a single molecule binds to each vertex, thereby blocking the attachment of EV-A71 to the host cells.
Journal ArticleDOI
Calix[n]arene-based drug carriers: A DFT study of their electronic interactions with a chemotherapeutic agent used against leukemia
Rodrigo Galindo-Murillo,Alberto Olmedo-Romero,Eduardo Cruz-Flores,Petronela M. Petrar,Sándor Kunsági-Máté,Joaquín Barroso-Flores +5 more
TL;DR: In this paper, the suitability of eight differently substituted calix[n]arenes (with R =-OEt; SO3H and n = 4, 5, 6, 8) as drug delivery agents for 3-phenyl-1H-[1]benzofuro[3,2-c]pyrazole (henceforth referred as GTP), a promising new tyrosine kinase inhibitor drug, has been analyzed by means of DFT theoretical calculations at the B97D/6-31G(d,p) level of theory
Journal ArticleDOI
Detailed Per-residue Energetic Analysis Explains the Driving Force for Microtubule Disassembly.
TL;DR: All-atom molecular dynamics simulations for arbitrarily long microtubules that have either GDP or GTP molecules in the E-site of β-tubulin showed that the microtubule seam is the most energetically labile inter-dimer interface and could serve as a trigger point for disassembly.
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.