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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Understanding the dissolution of softwood lignin in ionic liquid and water mixed solvents.
TL;DR: In this article, a cosolvent-based approach to understand the dissolution of lignin with 61 guaiacyl subunits at the molecular level was reported, where atomistic molecular dynamics simulations were performed in 0, 20, 50, 80, and 100% 1-Ethyl-3-Methylimidazolium acetate (EmimOAc) systems.
Journal ArticleDOI
Phosphonium carbosilane dendrimers for biomedical applications – synthesis, characterization and cytotoxicity evaluation
Tomáš Strašák,Jan Malý,Dominika Wrobel,Marek Malý,Regina Herma,Jan Čermák,Monika Müllerová,Lucie Červenková Št′astná,Petra Cuřínová +8 more
TL;DR: Phosphonium carbosilane dendrimers could represent a valuable alternative to ammonium ones in gene therapy applications due to comparable or lower cytotoxicities, the presence of positive charge for nucleic acid electrostatic binding and in the cases of P(C6H4-OMe)3 and P(Ph)3 d endrimers high potential of mitochondrial targeting.
Journal ArticleDOI
Isolation of Antidiabetic Withanolides from Withania coagulans Dunal and Their In Vitro and In Silico Validation.
Saima Maher,M. Iqbal Choudhary,M. Iqbal Choudhary,Farooq Saleem,Saima Rasheed,Imran Waheed,Sobia Ahsan Halim,Muhammad Azeem,Iskandar Abdullah,Matheus Froeyen,Muhammad Usman Mirza,Sarfraz Ahmad +11 more
TL;DR: This study provides basis to discover specific antidiabetic compounds from W. coagulans by identifying a new withanolide glycoside, withacogulanoside-B, from n-butanol extract and five known withanolides from chloroform extract.
Journal ArticleDOI
Solvation dynamics of N-substituted acrylamide polymers and the importance for phase transition behavior
TL;DR: Results can guide experimentalists and theoreticians to design new polymer structures with tailor-made LCST transitions while controlling the water solvation shell around the functional group.
Journal ArticleDOI
Biflavonoid-Induced Disruption of Hydrogen Bonds Leads to Amyloid-β Disaggregation
Peter K. Windsor,Stephen P. Plassmeyer,Dominic S. Mattock,Jonathan C. Bradfield,Erika Y. Choi,Bill R. Miller,Byung Hee Han +6 more
TL;DR: In this paper, the structural basis of amyloid β (Aβ) disaggregating activity of biflavonoids and their interactions at the atomic level was investigated, and molecular docking analysis showed that bifavonoids preferentially bind to the aromatic-rich, partially ordered N-termini of Aβ fibril via the π-π interactions.
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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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.