Journal ArticleDOI
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe,Thomas E. Cheatham +1 more
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
Citations
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Bioaccumulation in the gut and liver causes gut barrier dysfunction and hepatic metabolism disorder in mice after exposure to low doses of OBS.
TL;DR: Results indicate that the liver and gut are important target tissues for OBS exposure, and it is possible that high levels of bioaccumulation of OBS in the gut and liver might directly cause gut barrier dysfunction and hepatic metabolism disorder in mice.
Journal ArticleDOI
The Interaction of Heparin Tetrasaccharides with Chemokine CCL5 Is Modulated by Sulfation Pattern and pH
Arunima Singh,Warren C. Kett,India C. Severin,Isaac Agyekum,Jiana Duan,I. Jonathan Amster,Amanda E. I. Proudfoot,Deirdre R. Coombe,Robert J. Woods +8 more
TL;DR: Hemparin and tetrasaccharide fragments of heparin are able to inhibit CCL5-CCR1 binding, with IC50 values showing strong dependence on the pattern and extent of sulfation.
Journal ArticleDOI
Dynamic Structural Differences between Human and Mouse STING Lead to Differing Sensitivity to DMXAA
TL;DR: The results highlight the challenges in translating a mouse active STING compound into a human active compound, while also providing avenues to pursue for designing a small-molecule drug targeting human STING.
Journal ArticleDOI
L718Q mutant EGFR escapes covalent inhibition by stabilizing a non-reactive conformation of the lung cancer drug osimertinib.
Donatella Callegari,Kara E. Ranaghan,Christopher J. Woods,Roberta Minari,Marcello Tiseo,Marco Mor,Adrian J. Mulholland,Alessio Lodola +7 more
TL;DR: In this paper, the authors investigated the inhibitory process for EGFR T790M/L718Q by modeling the chemical step (i.e., alkylation of Cys797) using QM/MM simulations and the recognition step by MD simulations coupled with free-energy calculations.
Journal ArticleDOI
Unique residues in the ATP gated human P2X7 receptor define a novel allosteric binding pocket for the selective antagonist AZ10606120.
TL;DR: The characterisation of the allosteric pocket provides a new and novel target for rational P2X7R drug development and indicates that unique P2x7R features regulate access of AZ10606120 to theAllosteric site.
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.
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Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
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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.