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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Journal ArticleDOI
Rosette Nanotube Porins as Ion Selective Transporters and Single-Molecule Sensors
Prabhat Tripathi,Liang Shuai,Himanshu Joshi,Hirohito Yamazaki,William H. Fowle,Aleksei Aksimentiev,Hicham Fenniri,Meni Wanunu +7 more
TL;DR: Experimental observations of ion transport across 1.1 nm inner diameter RNT porins of various lengths reveals two distinct unbinding timescales, which suggest that interactions of either face of α-cyclodextrin with the RNTP face are differentiable, backed with all-atom molecular dynamics simulations.
Journal ArticleDOI
Disease-Homologous Mutation in the Cation Diffusion Facilitator Protein MamM Causes Single-Domain Structural Loss and Signifies Its Importance.
Shiran Barber-Zucker,René Uebe,Geula Davidov,Yotam Navon,Dror Sherf,Jordan H. Chill,Itamar Kass,Ronit Bitton,Dirk Schüler,Raz Zarivach +9 more
TL;DR: In vivo, in vitro and in silico studies indicate that the CTD fold is critical for CDF proteins’ proper function and support the previously suggested role of the CDF cytoplasmic domain as a CDF regulatory element.
Journal ArticleDOI
8-Oxoguanine Affects DNA Backbone Conformation in the EcoRI Recognition Site and Inhibits Its Cleavage by the Enzyme
J.J. Hoppins,D.R. Gruber,H.L. Miears,Alexey S. Kiryutin,Rustem D. Kasymov,Darya V. Petrova,Anton V. Endutkin,Alexander V. Popov,Alexandra V. Yurkovskaya,Stanislav O. Fedechkin,Stanislav O. Fedechkin,Jacob A. Brockerman,Jacob A. Brockerman,Dmitry O. Zharkov,Serge L. Smirnov +14 more
TL;DR: It is proposed that the disruption of enzymatic cleavage can be linked with the altered backbone conformation and dynamics in the free oxidized DNA substrate and, possibly, at the protein—DNA interface.
Architecture and self-assembly of the jumbo bacteriophage nuclear shell
Thomas G. Laughlin,Amar Deep,Amy Prichard,Christian Seitz,Yajie Gu,Eray Enustun,Sergey Suslov,Kanika Khanna,Erica A. Birkholz,Emily Armbruster,J. Andrew McCammon,Rommie E. Amaro,Joe Pogliano,Kevin D. Corbett,Elizabeth Villa +14 more
TL;DR: The architecture and assembly dynamics of the chimallin shell suggest mechanisms for its nucleation and growth, and its role as a scaffold for phage-encoded factors mediating macromolecular transport, cytoskeletal interactions, and viral maturation.
Journal ArticleDOI
Excited state Born-Oppenheimer molecular dynamics through coupling between time dependent DFT and AMOEBA.
TL;DR: The implementation of excited state Born-Oppenheimer molecular dynamics (BOMD) is presented using a polarizable QM/MM approach based on a time-dependent density functional theory (TDDFT) formulation and the AMOEBA force field, which confirms that such a conversion is governed by the twisting of the dimethylamino group.
References
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VMD: Visual molecular dynamics
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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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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.