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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On the contributing role of the transmembrane domain for subunit-specific sensitivity of integrin activation.
TL;DR: This work has identified a specific order of clasp disintegration upon TMD dissociation, which suggests that the closed state of integrins may comprise several microstates, and provides unprecedented insights into a possibly contributing role of TMD towards subunit-specific sensitivity of integrin activation.
Journal ArticleDOI
Potential Cancer- and Alzheimer's Disease-Targeting Phosphodiesterase Inhibitors from Uvaria alba: Insights from In Vitro and Consensus Virtual Screening.
Mark Tristan J. Quimque,Mark Tristan J. Quimque,Kin Israel Notarte,arianne letada,Rey Arturo T. Fernandez,Delfin Yñigo H. Pilapil,Kirstin Rhys S. Pueblos,Kirstin Rhys S. Pueblos,Jay Carl M. Agbay,Hans-Martin Dahse,Arlette Wenzel-Storjohann,Deniz Tasdemir,Deniz Tasdemir,Abbas Khan,Dong-Qing Wei,Allan Patrick G. Macabeo +15 more
TL;DR: In this paper, the authors evaluated anti-PDE4B along with antiproliferative and anti-cholinesterase activities of the extracts of the Philippine endemic species Uvaria alba using in vitro assays and framed the resulting biological significance through computational binding and reactivity-based experiments.
Journal ArticleDOI
Computationally Designed Cyclic Peptides Derived from an Antibody Loop Increase Breadth of Binding for Influenza Variants
Alexander M. Sevy,Alexander M. Sevy,Iuliia M. Gilchuk,Benjamin P. Brown,Nina G. Bozhanova,Rachel S. Nargi,Mattie Jensen,Jens Meiler,James E. Crowe,James E. Crowe +9 more
TL;DR: Cyclic peptides that mimic the heavy-chain complementarity-determining region 3 (CDRH3) of anti-influenza broadly neutralizing antibody C05 are designed and show that these peptides bound to HA molecules with <100 nM affinity, comparable with that of the full-length parental C05 IgG.
Journal ArticleDOI
Atomic structures of RNA nanotubes and their comparison with DNA nanotubes.
TL;DR: It is found that the RNTs are almost as stable as DNA nanotubes (DNTs), and both the terminal regions open up to give rise to a gating like behavior which can play a crucial role in drug delivery.
Journal ArticleDOI
Pathway and mechanism of drug binding to chemokine receptors revealed by accelerated molecular simulations
Shristi Pawnikar,Yinglong Miao +1 more
TL;DR: The newly identified allosteric site can be targeted for novel drug design targeting CXCR4 and other chemokine receptors, and is consistent with previous mutation experiments.
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
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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.