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
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Journal ArticleDOI
Active Site Breathing of Human Alkbh5 Revealed by Solution NMR and Accelerated Molecular Dynamics.
Jeffrey A. Purslow,Trang T. Nguyen,Timothy K. Egner,Rochelle R. Dotas,Balabhadra Khatiwada,Vincenzo Venditti +5 more
TL;DR: The structural model reveals that Alkbh5 is more disordered in solution than what is observed in the crystal state and undergoes breathing motions that expand the active site and allow access to α-ketoglutarate.
Journal ArticleDOI
The Pivotal Role of Protein Phosphorylation in the Control of Yeast Central Metabolism.
Panayotis Vlastaridis,Athanasios Papakyriakou,Anargyros Chaliotis,Efstratios Stratikos,Stephen G. Oliver,Grigorios D. Amoutzias +5 more
TL;DR: A compendium of highly confident protein phosphorylation sites (p-sites) for the model organism Saccharomyces cerevisiae has been analyzed and should enable the design of future high-throughput (HTP) mutation studies to identify key molecular switches/rheostats for the manipulation of not only the metabolism of yeast, but also that of many other biotechnologically and medically important fungi and eukaryotes.
Journal ArticleDOI
Electrostatic interaction-mediated conformational changes of adipocyte fatty acid binding protein probed by molecular dynamics simulation.
TL;DR: This work shows that R126A can generate a significant perturbation on structural stability of A-FABP, which implies that R 126 is of significance in inhibitor bindings, and can provide a theoretical guidance for design of potent inhibitors targeting A- FABP.
Journal ArticleDOI
In silico screening of antigenic B-cell derived T-cell epitopes and designing of a multi-epitope peptide vaccine for Acinetobacter nosocomialis
TL;DR: An in silico based proteome-wide screening for antigenic B-cell derived T-cell epitopes and their following use to design a multi-epitope peptide vaccine that can effectively engage the host immune system against Acinetobacter nosocomialis SSA3 strain is performed.
Journal ArticleDOI
Binding mechanism of inhibitors to p38α MAP kinase deciphered by using multiple replica Gaussian accelerated molecular dynamics and calculations of binding free energies
TL;DR: Results imply that residues V30, V38, L74, L75, I84, T106, H107, L108, M109, L167, F169 and D168 can be utilized as efficient targets of potent inhibitors toward p38α.
References
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VMD: Visual molecular dynamics
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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
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