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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Evaluation of the potency of FDA-approved drugs on wild type and mutant SARS-CoV-2 helicase (Nsp13).
Osman Mutluhan Ugurel,Ozal Mutlu,Emrah Sariyer,Sinem Kocer,Erennur Ugurel,Tugba Gul Inci,Oguz Ata,Dilek Turgut-Balik +7 more
TL;DR: Results suggest that the cangrelor, fludarabine, folic acid and polydatin were the most potent drugs which had potency to inhibit both the wild type and mutant SARS-CoV-2 helicase.
Journal ArticleDOI
Contributions of the membrane dipole potential to the function of voltage-gated cation channels and modulation by small molecule potentiators.
TL;DR: It is proposed that dynamic counter-balancing between Ψd and the transmembrane potential (ΔΨm) governs the conformational state transitions of voltage-gated ion channels, thereby increasing or decreasing the energy barriers governing channel gating transitions.
Journal ArticleDOI
Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory
Miki Nakano,Hisae Tateishi-Karimata,Shigenori Tanaka,Florence Tama,Osamu Miyashita,Shu-ichi Nakano,Naoki Sugimoto +6 more
TL;DR: The findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions.
Journal ArticleDOI
Critical Role of Interdomain Interactions in the Conformational Change and Catalytic Mechanism of Endoplasmic Reticulum Aminopeptidase 1.
Athanasios Stamogiannos,Zachary Maben,Athanasios Papakyriakou,Anastasia Mpakali,Paraskevi Kokkala,Dimitris Georgiadis,Lawrence J. Stern,Efstratios Stratikos +7 more
TL;DR: The findings suggest that electrostatic interactions between domains II and IV in ERAP1 are crucial for driving a conformational change that regulates the structural integrity of the catalytic site.
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Structure-based investigation of MARK4 inhibitory potential of Naringenin for therapeutic management of cancer and neurodegenerative diseases.
Saleha Anwar,Shama Khan,Anas Shamsi,Farah Anjum,Alaa Shafie,Asimul Islam,Faizan Ahmad,Imtaiyaz Hassan +7 more
TL;DR: In this article, Naringenin (NAG) has been shown to be a potent inhibitor of MAP/microtubule affinity-regulating kinase 4 (MARK4) using virtual high-throughput screening coupled with enzyme assay.
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.