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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Structural basis of lantibiotic recognition by the nisin resistance protein from Streptococcus agalactiae.
Sakshi Khosa,Benedikt Frieg,Daniel Mulnaes,Diana Kleinschrodt,Astrid Hoeppner,Holger Gohlke,Sander H. J. Smits +6 more
TL;DR: This work reports the first three-dimensional structure of a nisin resistance protein from Streptococcus agalactiae (SaNSR) at 2.2 Å resolution and determines the substrate specificity of SaNSR and ensures the exact coordination of the nisin cleavage site at the TASSAEM region.
Journal ArticleDOI
The lytic polysaccharide monooxygenase CbpD promotes Pseudomonas aeruginosa virulence in systemic infection
Fatemeh Askarian,Satoshi Uchiyama,Helen O. Masson,Henrik Vinther Sørensen,Ole Golten,Anne C. Bunæs,Sophanit Mekasha,Åsmund K. Røhr,Eirik Garpestad Kommedal,Judith Anita Ludviksen,Magnus Ø. Arntzen,Benjamin E. Schmidt,Raymond H. Zurich,Nina M. van Sorge,Nina M. van Sorge,Vincent G. H. Eijsink,Ute Krengel,Tom Eirik Mollnes,Nathan E. Lewis,Victor Nizet,Victor Nizet,Gustav Vaaje-Kolstad +21 more
TL;DR: CbpD, the LPMO of Pseudomonas aeruginosa, is a chitin-oxidizing virulence factor that promotes survival of the bacterium in human blood and attenuates the terminal complement cascade in human serum, and catalytic activity is crucial for virulence function.
Journal ArticleDOI
Maintaining and breaking symmetry in homomeric coiled-coil assemblies.
Guto G. Rhys,Christopher W. Wood,Eric J. M. Lang,Adrian J. Mulholland,R.L. Brady,Andrew R. Thomson,Derek N. Woolfson +6 more
TL;DR: It is shown that placing β-branched aliphatic residues along the lumen yields stable and open α-helical barrels, which is of interest for the rational design of functional proteins; whereas, the absence of β- Branched side chains leads to unusual low-symmetry α- helical bundles.
Journal ArticleDOI
CDR-H3 loop ensemble in solution - conformational selection upon antibody binding.
TL;DR: It is demonstrated for several examples that the conformation observed in the antibody crystal structure without antigen present is actually selected to bind the carboxyterminal tail region of the antigen-binding fragment (Fab), and the possibility that pre-existing conformations are present should always be considered.
Journal ArticleDOI
SUMOylation regulates LKB1 localization and its oncogenic activity in liver cancer
Imanol Zubiete-Franco,Juan L. García-Rodríguez,Fernando Lopitz-Otsoa,Marina Serrano-Macia,Jorge Simón,Pablo Fernández-Tussy,Lucía Barbier-Torres,David Fernández-Ramos,Virginia Gutiérrez-de-Juan,Sergio López de Davalillo,Onintza Carlevaris,Adolfo Beguiristain Gomez,Erica Villa,Diego F. Calvisi,César Martín,Edurne Berra,Patricia Aspichueta,Naiara Beraza,Marta Varela-Rey,Matías A. Avila,Manuel S. Rodriguez,José M. Mato,Irene Díaz-Moreno,Antonio Díaz-Quintana,Teresa C. Delgado,María L. Martínez-Chantar +25 more
TL;DR: It is found that in human hepatoma cells under hypoxic stress, L KB1 overexpression increases cell viability and aggressiveness in association with changes in LKB1 cellular localization and its oncogenic role in liver cancer.
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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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.