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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Elucidation of cryptic and allosteric pockets within the SARS-CoV-2 protease.
TL;DR: Using Gaussian accelerated molecular dynamics to enhance sampling of conformational space, cryptic pockets are identified within the SARS-CoV-2 main protease, including some within regions far from the active site and their druggability can aid in virtual screening efforts to identify a protease inhibitor for the treatment of COVID-19.
Journal ArticleDOI
ANO5 mutations in the Polish limb girdle muscular dystrophy patients: Effects on the protein structure
Adam Jarmuła,Anna Łusakowska,Jakub Piotr Fichna,Malgorzata Topolewska,Anna Macias,Katherine Johnson,Ana Töpf,Volker Straub,Edyta Rosiak,Krzysztof Szczepaniak,Stanislaw Dunin-Horkawicz,Aleksandra Maruszak,Anna Kamińska,Maria Jolanta Redowicz +13 more
TL;DR: The presented data indicate that the identified ANO5 mutations contribute to the observed muscle pathology and broaden the genetic spectrum of LGMD myopathies.
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Nuclear Magnetic Resonance of Single-Stranded RNAs and DNAs of CAAU and UCAAUC as Benchmarks for Molecular Dynamics Simulations.
TL;DR: Nuclear magnetic resonance spectra for RNA and DNA single strands, CAAU and UCAAUC, are used as benchmarks to test molecular dynamics simulations with AMBER force fields OL3 and ROC-RNA for RNA, and BSC1 for DNA.
Journal ArticleDOI
Designing a multi-epitope vaccine against Mycobacteroides abscessus by pangenome-reverse vaccinology.
Hamza Arshad Dar,Saba Ismail,Yasir Waheed,Sajjad Ahmad,Zubia Jamil,Hafsa Aziz,Helal F Hetta,Khalid Muhammad +7 more
TL;DR: In this paper, a multi-epitope based subunit vaccine was designed for Mycobacteroides abscessus using 34 complete genome sequences from the NCBI GenBank database.
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Estrogenic activity of benzotriazole UV stabilizers evaluated through in vitro assays and computational studies
TL;DR: The findings suggest that the endocrine disruption effects of BUVs are a cause for concern.
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
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
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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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Journal ArticleDOI
General definition of ring puckering coordinates
Dieter Cremer,John A. Pople +1 more
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