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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Solution structure of CXCL13 and heparan sulfate binding show that GAG binding site and cellular signalling rely on distinct domains.
Yoan R. Monneau,Lingjie Luo,Nehru Viji Sankaranarayanan,Balaji Nagarajan,Romain R. Vivès,Françoise Baleux,Umesh R. Desai,Fernando Arenzana-Seidedos,Hugues Lortat-Jacob +8 more
TL;DR: It is found that CXCL13 can be functionally presented to its receptor in a HS-bound form, suggesting that it can promote adhesion-dependent cell migration.
Journal ArticleDOI
Noncanonical α/γ Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field
Marie Zgarbová,Petr Jurečka,Pavel Banáš,Marek Havrila,Jiří Šponer,Jiří Šponer,Michal Otyepka +6 more
TL;DR: Molecular dynamics simulations of several prototypical RNA structures obtained from X-ray and NMR experiments, including canonical and mismatched RNA duplexes, UUCG and GAGA tetraloops, Loop E, the sarcin-ricin loop, a parallel guanine quadruplex, and a viral pseudoknot are presented.
Journal ArticleDOI
Computational approach to study the synthesis of noscapine and potential of stereoisomers against nsP3 protease of CHIKV.
Prashant Singh,Durgesh Kumar,Vijay Kumar Vishvakarma,Parul Yadav,Abhilash Jayaraj,Kamlesh Kumari +5 more
TL;DR: The integrated e-pharmacophore binding affinity based virtual screening, docking and molecular dynamics simulation recognized four hits isomers as inhibition nsP3 protease of CHIKV.
Journal ArticleDOI
Quantitative assessment of the determinant structural differences between redox-active and inactive glutaredoxins
Linda Liedgens,Jannik Zimmermann,Lucas Wäschenbach,Fabian Geissel,Hugo Laporte,Holger Gohlke,Holger Gohlke,Bruce A. Morgan,Marcel Deponte +8 more
TL;DR: The authors establish the molecular basis for glutaredoxin redox catalysis through comprehensive biochemical and structural analyses and elucidated the determinant structural differences between the two main classes of glutaredoxins.
Journal ArticleDOI
The first crystal structure of a DNA-free nuclear receptor DNA binding domain sheds light on DNA-driven allostery in the glucocorticoid receptor
TL;DR: The crystal structure of GR DBD in its DNA-free state is solved, the first such crystal structure from any nuclear receptor, and it is shown how DNA allosterically controls GR structure and dynamics.
References
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VMD: Visual molecular dynamics
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Journal ArticleDOI
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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.
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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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General definition of ring puckering coordinates
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