Journal ArticleDOI
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe,Thomas E. Cheatham +1 more
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
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Journal ArticleDOI
Revealing vilazodone's binding mechanism underlying its partial agonism to the 5-HT1A receptor in the treatment of major depressive disorder.
Guoxun Zheng,Guoxun Zheng,Weiwei Xue,Fengyuan Yang,Fengyuan Yang,Yang Zhang,Yang Zhang,Yu Zong Chen,Xiaojun Yao,Feng Zhu,Feng Zhu +10 more
TL;DR: This newly identified binding mechanism underlying vilazodone's partial agonism to the 5-HT1A receptor will provide valuable information for medicinal chemists working in the field of rational design of novel SPARIs for MDD treatment.
Journal ArticleDOI
Thiazole-based γ-building blocks as reverse-turn mimetic to design a gramicidin S analogue: conformational and biological evaluation.
Baptiste Legrand,Loïc Mathieu,Aurélien Lebrun,Soahary Andriamanarivo,Vincent Lisowski,Nicolas Masurier,Séverine Zirah,Young Kee Kang,Jean Martinez,Ludovic T. Maillard +9 more
TL;DR: The hybrid α,γ-cyclopeptide exhibited significant reduced haemotoxicity compared to gramicidin S, while maintaining strong antibacterial activity and NMR solution structure of the analogue adopted an antiparallel β-pleated sheet conformation similar to that of the natural compound.
Journal ArticleDOI
Molecular Dynamics-Markov State Model of Protein Ligand Binding and Allostery in CRIB-PDZ: Conformational Selection and Induced Fit.
TL;DR: In this article, the authors investigate protein-ligand binding and allostery based on a Markov state model (MSM) with states and rates obtained from all-atom MD simulations.
Journal ArticleDOI
Structure of a cleavage-independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer.
Anita Sarkar,Shridhar Bale,Anna-Janina Behrens,Sonu Kumar,Shailendra Kumar Sharma,N. de Val,Jesper Pallesen,Adriana Irimia,Devan Diwanji,Robyn L. Stanfield,Andrew B. Ward,Max Crispin,Max Crispin,Max Crispin,Richard T. Wyatt,Ian A. Wilson +15 more
TL;DR: Native-like soluble HIV envelope (Env) trimers are potential vaccine immunogens, and elimination of furin-dependence could provide a DNA-based alternative, so as to validate their potential as vaccine immunogen candidates.
Journal ArticleDOI
Assessment of Proton-Coupled Conformational Dynamics of SARS and MERS Coronavirus Papain-like Proteases: Implication for Designing Broad-Spectrum Antiviral Inhibitors
TL;DR: Simulations revealed that the BL2 can open and close depending on the protonation state of C271/270, consistent with the most recent crystal structure evidence, and the calculated pKa’s support the catalytic roles of the Cys–His–Asp triad.
References
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VMD: Visual molecular dynamics
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Journal ArticleDOI
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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.
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General definition of ring puckering coordinates
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