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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Vaccinomics to design a novel single chimeric subunit vaccine for broad-spectrum immunological applications targeting nosocomial Enterobacteriaceae pathogens.
TL;DR: A multi-epitope peptide vaccine construct formulated comprising predicted epitopes with potential to evoke both innate and adaptive immunity and B-subunit of cholera toxin as an adjuvant is believed to be highly useful for vaccinologists in making a highly effective vaccine for E. cloacae specifically.
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Discovery and Biological Evaluation of a Novel Highly Potent Selective Butyrylcholinsterase Inhibitor.
Qi Li,Shuaishuai Xing,Ying Chen,Qinghong Liao,Baichen Xiong,Siyu He,Weixuan Lu,Yang Liu,Hongyu Yang,Qihang Li,Feng Feng,Wenyuan Liu,Yao Chen,Haopeng Sun +13 more
TL;DR: Treatment with 8012-9656 could almost entirely recover the Aβ1-42 (icv)-impaired cognitive function to normal level and showed better behavioral performance than donepezil.
Journal ArticleDOI
Acceleration of biomolecular kinetics in Gaussian accelerated molecular dynamics.
TL;DR: Gaussian accelerated molecular dynamics is examined using alanine dipeptide in explicit solvent as a biomolecular model system and Kramers' rate theory was applied to estimate GaMD acceleration using simulation-derived diffusion coefficients, curvatures and barriers of free energy profiles.
Journal ArticleDOI
Structural mechanism of helicase loading onto replication origin DNA by ORC-Cdc6
Zuanning Yuan,Sarah Schneider,Thomas Dodd,Alberto Riera,Lin Bai,Chunli Yan,Indiana Magdalou,Ivaylo Ivanov,Bruce Stillman,Huilin Li,Christian Speck +10 more
TL;DR: Two cryo-electron microscopy structures that capture helicase loader–helicase complexes just prior to DNA insertion in budding yeast provide crucial insights into the mechanism required for topologically linking the helicase to DNA.
Journal ArticleDOI
Systematic Parametrization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models.
TL;DR: Parameter scanning for the 12-6 Lennard-Jones nonbonded model of divalent metal ions is performed in conjunction with the four new water models as well as the four previous water models to find that these new three-point and four-point water models provide comparable or significantly improved performance for the simulation of d subjective metal ions when compared to previousWater models in the same category.
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
CHARMM: the biomolecular simulation program.
Bernard R. Brooks,Charles L. Brooks,Alexander D. MacKerell,Lennart Nilsson,Robert J. Petrella,Benoît Roux,Youngdo Won,Georgios Archontis,Christian Bartels,Stefan Boresch,Amedeo Caflisch,Leo S. D. Caves,Qiang Cui,Aaron R. Dinner,Michael Feig,Stefan Fischer,Jiali Gao,Milan Hodošček,Wonpil Im,K. Kuczera,Themis Lazaridis,Jianpeng Ma,V. Ovchinnikov,Emanuele Paci,Richard W. Pastor,Carol Beth Post,Jingzhi Pu,M. Schaefer,Bruce Tidor,Richard M. Venable,H. L. Woodcock,Xiongwu Wu,Wei Yang,Darrin M. York,Martin Karplus,Martin Karplus +35 more
TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.
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.