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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Towards A Novel Multi-Epitopes Chimeric Vaccine for Simulating Strong Immune Responses and Protection against Morganella morganii.
Asad Ullah,Sajjad Ahmad,Saba Ismail,Zobia Afsheen,Muhammad Khurram,Muhammad Tahir ul Qamar,Naif AlSuhaymi,Mahdi H. Alsugoor,Khaled S Allemailem +8 more
TL;DR: In this paper, a multi-epitope-based vaccine against M. morganii was proposed, where the predicted proteins from fully sequenced genomes of the pathogen were subjected to a core sequences analysis, followed by the prioritization of non-redundant, host nonhomologous and extracellular, outer membrane and periplasmic membrane virulent proteins as vaccine targets.
Journal ArticleDOI
Investigating changes in the gas-phase conformation of Antithrombin III upon binding of Arixtra using traveling wave ion mobility spectrometry (TWIMS)
Yuejie Zhao,Arunima Singh,Lingyun Li,Robert J. Linhardt,Yongmei Xu,Jian Liu,Robert J. Woods,I. Jonathan Amster +7 more
TL;DR: The first travelling wave ion mobility mass spectrometry (TWIMS) investigation of the conformational changes in ATIII induced by its interaction with Arixtra proves the capability of TWIMS to retain the significant features of the solution structure of a protein-carbohydrate complex so that it can be used to study protein conformationalChanges induced by the binding of glycosaminoglycan ligands.
Journal ArticleDOI
Self-Assembly of a Designed Nucleoprotein Architecture through Multimodal Interactions
Rohit H. Subramanian,Sarah J. Smith,Robert G. Alberstein,Jake B. Bailey,Ling Zhang,Giovanni Cardone,Lauri Suominen,Mohamed Chami,Henning Stahlberg,Timothy S. Baker,F. Akif Tezcan +10 more
TL;DR: A structurally well-defined synthetic nucleoprotein assembly is reported that forms through the synergy of three types of intermolecular interactions: Watson–Crick base pairing, NA–protein interactions, and protein–metal coordination.
Journal ArticleDOI
The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA
TL;DR: It is demonstrated that 20–30% DNA extension is sufficient for breaking B-DNA around and significantly above cellular supercoiling, and that the DNA sequence is crucial for understanding structural changes under mechanical stress.
Journal ArticleDOI
Design, synthesis, biological evaluation, and molecular modeling studies of quinoline-ferulic acid hybrids as cholinesterase inhibitors.
Jun Mo,Hongyu Yang,Tingkai Chen,Qihang Li,Hongzhi Lin,Feng Feng,Wenyuan Liu,Wei Qu,Qinglong Guo,Heng Chi,Yao Chen,Haopeng Sun +11 more
TL;DR: A new chemotype of multifunctional hybrid is reported, which may be further modified to develop new anti-Alzheimer's agents and is confirmed against H2O2-induced oxidative damage towards PC12 cells.
References
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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
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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.
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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.