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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In Vitro Antidiabetic, Anti-Obesity and Antioxidant Analysis of Ocimum basilicum Aerial Biomass and in Silico Molecular Docking Simulations with Alpha-Amylase and Lipase Enzymes.
Zoy I. Noor,Dildar Ahmed,Hafiz Muzzammel Rehman,Muhammad Tariq Qamar,Matheus Froeyen,Sarfraz Ahmad,Muhammad Usman Mirza +6 more
TL;DR: The in-silico molecular docking study showed linalool and estragole to have considerable PPA and PPL binding potential, which were further investigated through molecular dynamics simulations and binding free energy calculations.
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ATP Controls the Aggregation of Aβ16–22 Peptides
Saikat Pal,Sandip Paul +1 more
TL;DR: It is assumed that the deficiency of ATP may cause Alzheimer disease (AD) because biological molecule ATP interacts with Aβ16-22 peptide via hydrogen bond, π-π stacking and NH-π interactions which, ultimately, prevents the aggregation of A β16- 22 peptide.
Journal ArticleDOI
Ethidium bromide interactions with DNA: an exploration of a classic DNA-ligand complex with unbiased molecular dynamics simulations.
TL;DR: In this article, the authors present molecular dynamics simulations of the interaction of ethidium with two different double-stranded DNA models, the first model system is the classic sequence d(CGCGAATTCGCG)2 also known as the DrewDickerson dodecamer.
Journal ArticleDOI
Nanoscale Structure and Elasticity of Pillared DNA Nanotubes
TL;DR: An atomistic model of pillared DNA nanotubes (DNTs) and their elastic properties are presented and a gradual increase of persistence length with an increasing number of pillars is found, in quantitative agreement with previous experimental findings.
Journal ArticleDOI
Potential Inhibitors of Galactofuranosyltransferase 2 (GlfT2): Molecular Docking, 3D-QSAR, and In Silico ADMETox Studies.
Christopher Llynard D. Ortiz,Christopher Llynard D. Ortiz,Gladys C. Completo,Ruel C. Nacario,Ricky B. Nellas +4 more
TL;DR: Computational methods such as molecular docking, receptor-ligand mapping, molecular dynamics, and Three-Dimensional-Quantitative Structure-Activity Relationship (3D-QSAR) were utilized to deduce the interactions of the reported compounds with the target enzyme, enabling the design of more potent GlfT2 inhibitors.
References
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VMD: Visual molecular dynamics
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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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