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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α-Glucosidase Inhibitors from Salvia circinata
TL;DR: A dried infusion prepared from the aerial parts of Salvia circinata showed poor hypoglycemic and antihyperglycemic effects when tested in normal and hyperglycemic mice using acute and oral glucose tolerance tests, respectively, suggesting the presence of α-glucosidase inhibitors in S. circinata.
Journal ArticleDOI
Molecular Mechanism of Binding Selectivity of Inhibitors toward BACE1 and BACE2 Revealed by Multiple Short Molecular Dynamics Simulations and Free-Energy Predictions.
TL;DR: In this work, multiple short molecular dynamics simulations are coupled with molecular mechanics generalized Born surface area (MM-GBSA) method to probe binding selectivity of three inhibitors DBO, CS9 and SC7 on BACE1 over BACE2, and the results show that the entropy effect plays a key role in selectivity identification of inhibitors toward Bace1 and Bace2.
Journal ArticleDOI
Trading off stability against activity in extremophilic aldolases.
Markus Dick,Oliver H. Weiergräber,Thomas Classen,Carolin Bisterfeld,Julia Bramski,Holger Gohlke,Jörg Pietruszka,Jörg Pietruszka +7 more
TL;DR: The first crystal structures of psychrophilic DERAs are presented, revealing a dimeric organization resembling their mesophilic but not their thermophilic counterparts, and suggesting a strategy for rational design of more durable enzyme variants.
Journal ArticleDOI
Investigation of the interactions of silibinin with 2-hydroxypropyl-β-cyclodextrin through biophysical techniques and computational methods.
Tahsin F. Kellici,Tahsin F. Kellici,Dimitrios Ntountaniotis,Georgios Leonis,Maria V. Chatziathanasiadou,Alexandra V. Chatzikonstantinou,Johanna Becker-Baldus,Clemens Glaubitz,Andreas G. Tzakos,Kyriakos Viras,Petros Chatzigeorgiou,Stavros Tzimas,Evangelia Kefala,Georgia Valsami,H.A. Archontaki,Manthos G. Papadopoulos,Thomas Mavromoustakos +16 more
TL;DR: It is pointed out that in both solid and liquid forms, the drug is engulfed and interacts with HP-β-CD in identical manner.
Journal ArticleDOI
HnRNP A1 Alters the Structure of a Conserved Enterovirus IRES Domain to Stimulate Viral Translation.
Michele Tolbert,Christopher E. Morgan,Marvin Pollum,Carlos E. Crespo-Hernández,Mei Ling Li,Gary Brewer,Blanton S. Tolbert +6 more
TL;DR: This work provides key details into how an EV71 IRES structure adapts to hijack a cellular protein, and it suggests that the SLII domain is a potential target for antiviral therapy.
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.