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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Mimicking the Chemistry of Natural Eumelanin Synthesis: The KE Sequence in Polypeptides and in Proteins Allows for a Specific Control of Nanosized Functional Polydopamine Formation.
Camille Bergtold,Camille Bergtold,Daniel Hauser,Alain Chaumont,Salima El Yakhlifi,Mihaela Mateescu,Florent Meyer,Florent Meyer,Marie-Hélène Metz-Boutigue,Marie-Hélène Metz-Boutigue,Benoît Frisch,Pierre Schaaf,Pierre Schaaf,Dris Ihiawakrim,Ovidiu Ersen,Christophe A. Monnier,Alke Petri-Fink,Barbara Rothen-Rutishauser,Vincent Ball,Vincent Ball +19 more
TL;DR: It is shown that a specific diad of amino acids in proteins, namely KE, allows for specific control in the oxidation-self-assembly of dopamine to obtain polydopamine@protein core-shell nanoparticles which are biocompatible.
Journal ArticleDOI
Catalytic Mechanism of Human Ten-Eleven Translocation-2 (TET2) Enzyme: Effects of Conformational Changes, Electric Field, and Mutations
TL;DR: Ten-eleven translocation (TET) family of enzymes are non-heme Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenases that perform oxidation of the methyl group of the 5-methylcytosine on DNA.
Journal ArticleDOI
Identification of new BACE1 inhibitors using Pharmacophore and Molecular dynamics simulations approach
TL;DR: Results from glide XP docking and induced fit docking showed that four leads have good interactions with the target protein in comparison with cocrystal (amino-ethylene Bace1 inhibitor), and molecular dynamics simulation for these leads bound with BACE1 shows conformational stability and difference in dynamical flap behaviors of the active site with cocystal inhibitor.
Journal ArticleDOI
Structure and dynamics of ionic liquid tolerant hyperthermophilic endoglucanase Cel12A from Rhodothermus marinus
Bharat Manna,Amit Ghosh +1 more
TL;DR: The molecular understanding behind the origin of activity loss of RmCel12A is revealed and proposed insights for the further improvement of IL sensitivity are proposed.
Journal ArticleDOI
Multitarget Anticancer Agents Based on Histone Deacetylase and Protein Kinase CK2 inhibitors.
Regina Martínez,Bruno Di Geronimo,Miryam Pastor,José María Zapico,Claire Coderch,R. R. Panchuk,N. R. Skorokhyd,Maciej Masłyk,Ana Ramos,Beatriz de Pascual-Teresa +9 more
TL;DR: The design of multi-targeting histone deacetylase (HDAC) and protein kinase CK2 inhibitors as a novel therapeutic strategy against cancer is communicated and new multitarget inhibitors have been designed and synthesized.
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.
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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.