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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Computational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 protease against COVID-19.
TL;DR: The combination of three known drugs, lopinavir, oseltamivir and ritonavir has been proposed to control the virulence to a great extent in COVID-19 affected patients within 48 hours and showed a better binding energy than that of individual drugs.
Journal ArticleDOI
Assessing the Current State of Amber Force Field Modifications for DNA
Rodrigo Galindo-Murillo,James C. Robertson,Marie Zgarbová,Jiří Šponer,Jiří Šponer,Michal Otyepka,Petr Jurečka,Thomas E. Cheatham +7 more
TL;DR: A direct comparison of two of the most recent and state-of-the-art Amber force field modifications, bsc1 and OL15, that focus on accurate modeling of double-stranded DNA, concludes that both modifications are a remarkable improvement over the previous bsc0 force field.
Journal ArticleDOI
Identification of Phosphorylation Codes for Arrestin Recruitment by G Protein-Coupled Receptors
X. Edward Zhou,X. Edward Zhou,Yuanzheng He,Parker W. de Waal,Xiang Gao,Yanyong Kang,Ned Van Eps,Yanting Yin,Yanting Yin,Kuntal Pal,Devrishi Goswami,Thomas A. White,Anton Barty,Naomi R. Latorraca,Henry N. Chapman,Wayne L. Hubbell,Ron O. Dror,Raymond C. Stevens,Raymond C. Stevens,Vadim Cherezov,Vsevolod V. Gurevich,Patrick R. Griffin,Oliver P. Ernst,Karsten Melcher,H. Eric Xu,H. Eric Xu +25 more
TL;DR: An X-ray free electron laser (XFEL) crystal structure of the rhodopsin-arrestin complex is reported, in which the phosphorylated C terminus of r Rhodopsin forms an extended intermolecular β sheet with the N-terminal β strands of arrestin.
Journal ArticleDOI
Crystal Structure of an LSD-Bound Human Serotonin Receptor
Daniel Wacker,Sheng Wang,John D. McCorvy,Robin M. Betz,AJ Venkatakrishnan,Anat Levit,Katherine Lansu,Zachary L. Schools,Tao Che,David E. Nichols,Brian K. Shoichet,Ron O. Dror,Bryan L. Roth +12 more
TL;DR: The crystal structure of LSD in complex with the human serotonin receptor 5-HT2B reveals conformational rearrangements to accommodate LSD, providing a structural explanation for the conformational selectivity of LSD's key diethylamide moiety.
Journal ArticleDOI
Identification of chymotrypsin-like protease inhibitors of SARS-CoV-2 via integrated computational approach.
TL;DR: Computational drug design methods were applied to identify Chymotrypsin-like protease inhibitors from FDA approved antiviral drugs and an in-house database of natural and drug-like compounds of synthetic origin and results indicate that the identified compounds can inhibit the function of Chymosorbic protease of Coronavirus.
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.
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.