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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A complex structure of arrestin-2 bound to a G protein-coupled receptor.
Wanchao Yin,Zhihai Li,Mingliang Jin,Yanting Yin,P.W. de Waal,Kuntal Pal,Kuntal Pal,Yulong Yin,Yulong Yin,Xiang Gao,Yuanzheng He,Yuanzheng He,Jing Gao,Xiaoxi Wang,Yan Zhang,Hu Zhou,Karsten Melcher,Yi Jiang,Yao Cong,X. Edward Zhou,Xuekui Yu,H. Eric Xu,H. Eric Xu +22 more
TL;DR: The structure of Arr2 in complex with neurotensin receptor 1 (NTSR1) is reported, which reveals an overall assembly that is strikingly different from the visual arrestin–rhodopsin complex by a 90° rotation of ArR2 relative to the receptor.
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Colibactin DNA-damage signature indicates mutational impact in colorectal cancer.
Paulina J. Dziubańska-Kusibab,Hilmar Berger,Federica Battistini,Britta A. M. Bouwman,Amina Iftekhar,Riku Katainen,Tatiana Cajuso,Nicola Crosetto,Modesto Orozco,Lauri A. Aaltonen,Thomas F. Meyer +10 more
TL;DR: Identification of a DNA-damage signature induced by colibactin, a toxin expressed by some strains of Escherichia coli, is enriched in human colorectal cancers.
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Smoothened stimulation by membrane sterols drives Hedgehog pathway activity
Ishan Deshpande,Jiahao Liang,Danielle S. Hedeen,Kelsey J. Roberts,Yunxiao Zhang,Betty Ha,Naomi R. Latorraca,Bryan Faust,Ron O. Dror,Philip A. Beachy,Benjamin R. Myers,Benjamin R. Myers,Aashish Manglik +12 more
TL;DR: The crystal structure of active mouse SMO in complex with the SAG21k agonist and a stabilizing intracellular binding nanobody reveals the structural basis of SMO regulation by PTCH1, and suggests a strategy for overcoming clinical resistance to SMO inhibitors.
Journal ArticleDOI
The Bio3D packages for structural bioinformatics
TL;DR: The Bio3D‐eddm package supports both experimental and theoretical simulation‐generated structures, is integrated with other methods for dissecting sequence‐structure–function relationships, and can be used in a highly automated and reproducible manner.
Journal ArticleDOI
Molecular mechanism of biased signaling in a prototypical G protein-coupled receptor.
Carl-Mikael Suomivuori,Naomi R. Latorraca,Laura M. Wingler,Laura M. Wingler,Stephan Eismann,Matthew C. King,Alissa L. W. Kleinhenz,Alissa L. W. Kleinhenz,Alissa L. W. Kleinhenz,Meredith A. Skiba,Dean P. Staus,Dean P. Staus,Andrew C. Kruse,Robert J. Lefkowitz,Robert J. Lefkowitz,Ron O. Dror +15 more
TL;DR: Detailed atomic-level molecular dynamics simulations are used to determine how arrestin bias and G protein bias arise at the angiotensin II type 1 receptor and designed ligands with desired signaling profiles.
References
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VMD: Visual molecular dynamics
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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.
Journal ArticleDOI
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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.