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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Molecular Determinants for Unphosphorylated STAT3 Dimerization Determined by Integrative Modeling
Jacopo Sgrignani,Simon Olsson,Dariusz Ekonomiuk,Davide Genini,Rolf Krause,Carlo V. Catapano,Andrea Cavalli,Andrea Cavalli +7 more
TL;DR: An integrated modeling study of STAT3, a member of the STAT family of utmost importance in cancer development and therapy, is presented, in which available experimental data is combined with several computational methodologies such as homology modeling, protein-protein docking, and molecular dynamics to build reliable atomistic models of USTAT3 dimers.
Journal ArticleDOI
The influence of structured interfacial water on the photoluminescence of carboxyester‐terminated oligo‐p‐phenylene ethynylenes
TL;DR: In this paper, the influence of interfacial water on the photophysical properties of a carboxyester-substituted compound in this class through analysis of the aggregation with ionic surfactants, solvent isotope effects, and classical molecular dynamics simulations was examined.
Journal ArticleDOI
Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes.
TL;DR: Free energy calculations based on all-atom molecular dynamics simulations are applied to predict the changes in binding free energy for all single base pair perturbations of the binding sites for four eukaryotic transcription factors for which high-quality experimental data exist.
Journal ArticleDOI
Effects of protein-protein interactions and ligand binding on the ion permeation in KCNQ1 potassium channel
TL;DR: The results reveal that interactions between KCNQ1 with KCNE1 causes a pore constriction in the former, which in-turn forms small energetic barriers in the ion-permeation pathway, which indicates that the SMD simulations have been able to discern between strong and week blockers and reveal their influence on potassium ion permeation.
Journal ArticleDOI
Toward wide-spectrum antivirals against coronaviruses: Molecular characterization of SARS-CoV-2 NSP13 helicase inhibitors
TL;DR: In this paper , molecular dynamics simulations are used to unravel the SARS-CoV-2 NSP13 behavior in interaction with natural ligands and inhibitors, and the results show that the NSP-13 behavior is not consistent with the observed behavior of natural ligand-and inhibitor interactions.
References
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VMD: Visual molecular dynamics
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Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
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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.
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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.