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
Structure and mechanism of the cation-chloride cotransporter NKCC1.
Thomas A. Chew,Benjamin J. Orlando,Jinru Zhang,Naomi R. Latorraca,Amy Wang,Scott A. Hollingsworth,Dong-Hua Chen,Ron O. Dror,Maofu Liao,Liang Feng +9 more
TL;DR: The cryo-EM structure of the zebrafish cation–chloride cotransporter NKCC1 reveals the domain organization, ion translocation pathway, ion-binding sites and key residues for binding activity, providing insights into the activity of this family of transporter proteins with key roles in physiology.
Journal ArticleDOI
Temperature-Sensitive Substrate and Product Binding Underlie Temperature-Compensated Phosphorylation in the Clock
Yuta Shinohara,Yohei M. Koyama,Maki Ukai-Tadenuma,Takatsugu Hirokawa,Takatsugu Hirokawa,Masaki Kikuchi,Rikuhiro G. Yamada,Hideki Ukai,Hiroshi Fujishima,Takashi Umehara,Kazuki Tainaka,Kazuki Tainaka,Hiroki R. Ueda,Hiroki R. Ueda +13 more
TL;DR: Temperature compensation is a striking feature of the circadian clock and biochemical mechanisms underlying temperature-compensated, CKIδ-dependent multi-site phosphorylation in mammals are investigated, suggesting the temperature-sensitive substrate- and product-binding mechanisms underlie temperature compensation.
Journal ArticleDOI
On the absence of intrahelical DNA dynamics on the μs to ms timescale
TL;DR: Long timescale molecular dynamics simulations of a B-DNA duplex structure that addresses the hypothesis that the absence of motion on this timescale would present a “static” DNA sequence-specific structure that matches the encounter timescales of proteins, thereby facilitating recognition.
Journal ArticleDOI
Sampling alternative conformational states of transporters and receptors with AlphaFold2
TL;DR: An approach to drive AF2 to sample alternative conformations of topologically diverse transporters and G-protein-coupled receptors that are absent from the AF2 training set is presented, suggesting a straightforward approach to identifying native-like alternative states, while also highlighting the need for the next generation of deep learning algorithms to be designed to predict ensembles of biophysically relevant states.
Journal ArticleDOI
General Purpose Water Model Can Improve Atomistic Simulations of Intrinsically Disordered Proteins
TL;DR: It is demonstrated that OPC, together with a popular AMBER force field ff99SB, offers a noticeable improvement over TIP3P in producing more realistic structural ensembles of three common IDPs benchmarks, which, it is argued, is consistent with its biological function as facilitator of internucleosome interactions.
References
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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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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.