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
Citations
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Journal ArticleDOI
Plant-derived natural polyphenols as potential antiviral drugs against SARS-CoV-2 via RNA-dependent RNA polymerase (RdRp) inhibition: an in-silico analysis.
TL;DR: It is suggested that EGCG, TF2a,TF2b, TF3 can inhibit RdRp and represent an effective therapy for COVID-19, and the binding free energy components calculated by the MM-PBSA also confirm the stability of the complexes.
Book ChapterDOI
Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications
TL;DR: The theory of GaMD is presented, its implementation in the widely used molecular dynamics software packages (AMBER and NAMD), and applications to the alanine dipeptide biomolecular model system, protein folding, biomolescular large-scale conformational transitions and biomolecules recognition are presented.
Journal ArticleDOI
Structure–Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling
TL;DR: Calculation of the kinetic rate constants determining each step in the permeation event allows derivation of structure-kinetic relationships of permeation, and this work finds that the desolvation/loss of hydrogen bonding required to leave the membrane partitioned position controls the membrane flip-flop rate, whereas membrane partitioning determines the rate of leaving the membrane.
Journal ArticleDOI
Exploring the Binding Mechanism of Metabotropic Glutamate Receptor 5 Negative Allosteric Modulators in Clinical Trials by Molecular Dynamics Simulations
Tingting Fu,Tingting Fu,Guoxun Zheng,Guoxun Zheng,Gao Tu,Gao Tu,Fengyuan Yang,Fengyuan Yang,Yu Zong Chen,Xiaojun Yao,Xiaofeng Li,Xiaofeng Li,Weiwei Xue,Feng Zhu,Feng Zhu +14 more
TL;DR: This comprehensive study presented a better understanding of mGlu5 receptor NAMs binding mechanism, which would be further used as a useful framework to assess and discover novel lead scaffolds for N AMs.
Journal ArticleDOI
Virtual screening-driven drug discovery of SARS-CoV2 enzyme inhibitors targeting viral attachment, replication, post-translational modification and host immunity evasion infection mechanisms.
Mark Tristan J. Quimque,Mark Tristan J. Quimque,Kin Israel Notarte,Rey Arturo T. Fernandez,Mark Andrew O. Mendoza,Rhenz Alfred D Liman,Justin Allen K. Lim,Luis Agustin E. Pilapil,Jehiel Karsten H. Ong,Adriel M. Pastrana,Abbas Khan,Dong-Qing Wei,Allan Patrick G. Macabeo +12 more
TL;DR: Nine antiviral secondary metabolites from fungi were docked onto five SARS-CoV2 enzymes involved in viral attachment, replication, post-translational modification, and host immunity evasion infection mechanisms followed by molecular dynamics simulation and in silico ADMET prediction.
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
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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.