Journal ArticleDOI
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe,Thomas E. Cheatham +1 more
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
A Comparative Insight into Amprenavir Resistance of Mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 Protease Based on Thermodynamic Integration and MM-PBSA Methods
TL;DR: The present study could provide important guidance for the design of new potent inhibitors that could alleviate drug resistance of PR due to mutations by revealing that these mutations can adjust the shape and conformation of the binding pocket which provides main contributions to the decrease in the van der Waals interactions of APV with mutated PRs.
Journal ArticleDOI
Small-Molecule Covalent Modification of Conserved Cysteine Leads to Allosteric Inhibition of the TEAD⋅Yap Protein-Protein Interaction
Khuchtumur Bum-Erdene,Donghui Zhou,Giovanni Gonzalez-Gutierrez,Mona K. Ghozayel,Yubing Si,David Xu,Harlan E. Shannon,Barbara J. Bailey,Timothy W. Corson,Karen E. Pollok,Clark D. Wells,Samy O. Meroueh +11 more
TL;DR: Small-molecule TEAD⋅Yap inhibitors that rapidly and selectively form a covalent bond with a conserved cysteine located within the unique deep hydrophobic palmitate-binding pocket of TEADs are reported.
Journal ArticleDOI
Marine natural compounds as potents inhibitors against the main protease of SARS-CoV-2-a molecular dynamic study.
Muhammad Tahir Khan,Arif Ali,Qiankun Wang,Muhammad Irfan,Abbas Khan,Muhammad Zeb,Yu Juan Zhang,Sathishkumar Chinnasamy,Dong-Qing Wei +8 more
TL;DR: Marine natural compounds may be used as a potential inhibitor against SARS-CoV-2 for better management of COVID-19, a single-stranded RNA virus responsible for severe acute respiratory disease.
Journal ArticleDOI
Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations.
TL;DR: Dynamics analyses based on MD trajectories indicate that mutations not only regulate the structural flexibility but also change the internal motion modes of GR, which implies that the aptamer domain activity of GR is extremely plastic and thus readily tunable by nucleotide mutations.
Journal ArticleDOI
Cyclin-dependent kinase 12 is a drug target for visceral leishmaniasis
Susan Wyllie,Michael G. Thomas,Stephen Patterson,Sabrinia D. Crouch,Manu De Rycker,Rhiannon Lowe,Stephanie Gresham,Michael D. Urbaniak,Michael D. Urbaniak,Thomas D. Otto,Thomas D. Otto,Laste Stojanovski,Frederick R. C. Simeons,Sujatha Manthri,Lorna MacLean,Fabio Zuccotto,Nadine Homeyer,Hannah Pflaumer,Markus Boesche,Lalitha Sastry,Paul Connolly,Sebastian Albrecht,Matthew Berriman,Gerard Drewes,David W. Gray,Sonja Ghidelli-Disse,Susan Dixon,Jose M. Fiandor,Paul G. Wyatt,Michael A. J. Ferguson,Alan H. Fairlamb,Timothy J. Miles,Kevin D. Read,Ian H. Gilbert +33 more
TL;DR: Development of an anti-leishmanial drug-like chemical series based on a pyrazolopyrimidine scaffold is described, and cdc2-related kinase 12 (CRK12) is identified as the probable primary drug target for visceral leishmaniasis.
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.