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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Polyreactive Broadly Neutralizing B cells Are Selected to Provide Defense against Pandemic Threat Influenza Viruses
Jenna J. Guthmiller,Linda Yu-Ling Lan,Monica L. Fernández-Quintero,Julianna Han,Henry A. Utset,Dalia J. Bitar,Natalie J. Hamel,Olivia Stovicek,Lei Li,Micah E. Tepora,Carole Henry,Karlynn E. Neu,Haley L. Dugan,Marta T. Borowska,Yao-Qing Chen,Sean T. H. Liu,Christopher T. Stamper,Nai-Ying Zheng,Min Huang,Anna-Karin E. Palm,Adolfo García-Sastre,Raffael Nachbagauer,Peter Palese,Lynda Coughlan,Lynda Coughlan,Florian Krammer,Andrew B. Ward,Klaus R. Liedl,Patrick C. Wilson +28 more
TL;DR: By analyzing more than 500 monoclonal antibodies derived from B cells induced by numerous influenza virus vaccines and infections, it is found mAbs targeting conserved neutralizing influenza virus hemagglutinin epitopes were polyreactive.
ComponentDOI
Transcription preinitiation complex structure and dynamics provide insight into genetic diseases.
Chunli Yan,Thomas Dodd,Yuan He,John A. Tainer,John A. Tainer,Susan E. Tsutakawa,Ivaylo Ivanov +6 more
TL;DR: All available cryo-EM data is integrated to build a practically complete human PIC structural model that enables simulations that reveal the assembly's global motions, define PIC partitioning into dynamic communities and delineate how structural modules function together to remodel DNA.
Journal ArticleDOI
Effects of polymorphic variation on the mechanism of Endoplasmic Reticulum Aminopeptidase 1.
TL;DR: This work proposes that disease-associated SNPs can affect ERAP1 function by influencing substrate length selection and the conformational distribution of the protein ensemble, and provides novel insight on the mechanisms by which polymorphic variation distal from the active site of ERAP2 can translate to changes in function and contribute to immune system variability in humans.
Journal ArticleDOI
Gating-like Motions and Wall Porosity in a DNA Nanopore Scaffold Revealed by Molecular Simulations
TL;DR: All-atom molecular dynamics simulations of a DNA nanotube (DNT) pore scaffold are reported to gain fundamental insight into its atomic structure, dynamics, and interactions with ions and water.
Journal ArticleDOI
Cellulose Crystal Dissolution in Imidazolium-Based Ionic Liquids: A Theoretical Study.
TL;DR: This work adopts a molecular dynamics approach to study the dissolution of model cellulose crystal structures in imidazolium-based ILs and gains deep mechanistic insights, demonstrating that dissolution involves IL penetration-induced cleavage of hydrogen bonds between cellulose molecular chains.
References
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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.