Journal ArticleDOI
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe,Thomas E. Cheatham +1 more
Reads0
Chats0
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
More filters
Journal ArticleDOI
In silico improvement of the cyanobacterial lectin microvirin and mannose interaction
Adonis de Melo Lima,Andrei Santos Siqueira,Marina Luiza Saraiva Moller,Rafael Conceição de Souza,Jorddy Neves Cruz,Alex Ranieri Jerônimo Lima,Ronaldo Correia da Silva,Délia Cristina Figueira Aguiar,João Lídio da Silva Gonçalves Vianez Júnior,Evonnildo Costa Gonçalves +9 more
TL;DR: The results of an in silico approach to improve affinity interaction between the cyanobacterial lectin microvirin and its ligand Manα(1-2)Man showed that the mutant (Thr82Arg) showed a higher affinity interaction with Manα (1- 2)Man.
Journal ArticleDOI
Structural insights into β-glucosidase transglycosylation based on biochemical, structural and computational analysis of two GH1 enzymes from Trichoderma harzianum.
Renata N. Florindo,Valquiria P. Souza,Hemily S. Mutti,Cesar M. Camilo,Livia Regina Manzine,Sandro R. Marana,Igor Polikarpov,Alessandro S. Nascimento +7 more
TL;DR: A close inspection of the enzymatic activity of these enzymes surprisingly revealed a marked difference between them despite the sequence similarity, with ThBgl1 has an increased tendency to catalyze transglycosylation reaction whileThBgl2 acts more as a hydrolyzing enzyme.
Journal ArticleDOI
Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome
Mehmet Ali Öztürk,Georgi V. Pachov,Rebecca C. Wade,Rebecca C. Wade,Rebecca C. Wade,Vlad Cojocaru +5 more
TL;DR: Brownian dynamics simulations of chromatosome assembly support the existence of both on- and off-dyad binding modes of gH5 and reveal alternative, sequence and conformation-dependent Chromatosome configurations, suggesting that the conformational dynamics of linker histones and nucleosomes facilitate alternative chromatosomes configurations through an interplay between induced fit and conformational selection.
Journal ArticleDOI
Investigation of the complexation between cyclodextrins and medetomidine enantiomers by capillary electrophoresis, NMR spectroscopy and molecular modeling.
TL;DR: The migration order of the enantiomers of medetomidine in the presence of cyclodextrins studied by capillary electrophoresis in phosphate buffer, pH 2.5, depended on the cavity size and the substitution pattern of the cyclodeXTrins.
Journal ArticleDOI
GLUT1 and GLUT3 involvement in anthocyanin gastric transport- Nanobased targeted approach.
Hélder Oliveira,Catarina Roma-Rodrigues,Ana Santos,Bruno Veigas,Natércia F. Brás,Ana Faria,Conceição Calhau,Victor de Freitas,Pedro V. Baptista,Nuno Mateus,Alexandra R. Fernandes,Iva Fernandes +11 more
TL;DR: The results support the involvement of GLUT1 and GLUT3 in the gastric absorption of anthocyanins with the importance of glucose on the transport regardless of its position or substitution pattern.
References
More filters
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
CHARMM: the biomolecular simulation program.
Bernard R. Brooks,Charles L. Brooks,Alexander D. MacKerell,Lennart Nilsson,Robert J. Petrella,Benoît Roux,Youngdo Won,Georgios Archontis,Christian Bartels,Stefan Boresch,Amedeo Caflisch,Leo S. D. Caves,Qiang Cui,Aaron R. Dinner,Michael Feig,Stefan Fischer,Jiali Gao,Milan Hodošček,Wonpil Im,K. Kuczera,Themis Lazaridis,Jianpeng Ma,V. Ovchinnikov,Emanuele Paci,Richard W. Pastor,Carol Beth Post,Jingzhi Pu,M. Schaefer,Bruce Tidor,Richard M. Venable,H. L. Woodcock,Xiongwu Wu,Wei Yang,Darrin M. York,Martin Karplus,Martin Karplus +35 more
TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.
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.