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
Structural Dynamics of Lateral and Diagonal Loops of Human Telomeric G-Quadruplexes in Extended MD Simulations.
TL;DR: A total of 217 μs of classical (unbiased) molecular dynamics simulations starting from the available solution structures of Htel GQs are carried out to characterize structural dynamics of the lateral and diagonal loops, using several recent AMBER DNA force-field variants.
Journal ArticleDOI
A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics.
Shweta Purawat,Shweta Purawat,Pek U Ieong,Robert D. Malmstrom,Garrett J. Chan,Alan K. Yeung,Ross C. Walker,Ross C. Walker,Ilkay Altintas,Ilkay Altintas,Rommie E. Amaro,Rommie E. Amaro +11 more
TL;DR: The presented workflow tool facilitates the management and deployment of large sets of MD simulations on heterogeneous computing resources and performs systematic analysis on the simulation outputs and enhances simulation reproducibility, execution scalability, and MD method development including benchmarking and validation.
Journal ArticleDOI
Calcium-Promoted Interaction between the C2-Domain Protein EHB1 and Metal Transporter IRT1 Inhibits Arabidopsis Iron Acquisition.
Imran Khan,Regina Gratz,Regina Gratz,Polina Denezhkin,Stephan Schott-Verdugo,Stephan Schott-Verdugo,Kalina Angrand,Lara Genders,Rubek Merina Basgaran,Claudia Fink-Straube,Tzvetina Brumbarova,Tzvetina Brumbarova,Holger Gohlke,Holger Gohlke,Petra Bauer,Petra Bauer,Rumen Ivanov,Rumen Ivanov +17 more
TL;DR: The data suggest that EHB1 acts as a direct inhibitor of IRT1-mediated iron import into the cell, a major step in understanding plant iron acquisition, a process that underlies the primary production of bioavailable iron for land ecosystems.
Journal ArticleDOI
Fc galactosylation follows consecutive reaction kinetics and enhances immunoglobulin G hexamerization for complement activation
Bingchuan Wei,Xuan Gao,Lance Cadang,Saeed Izadi,Peilu Liu,Peilu Liu,Hui-Min Zhang,Elizabeth S. Hecht,Jeongsup Shim,Gordon Magill,Juan Pablo Rincon Pabon,Juan Pablo Rincon Pabon,Lu Dai,Wilson Phung,Elaine Lin,Christopher Wang,Kevin Whang,Sean Sanchez,Jose Oropeza,Julien Camperi,Jennifer Zhang,Wendy Sandoval,Yonghua Taylor Zhang,Guoying Jiang +23 more
TL;DR: In this paper, the authors derived a kinetic model of galactose transfer reaction in the Golgi apparatus and used this model to determine the correlation between differently galactosylated species from Chinese hamster ovary (CHO) cell culture process.
Journal ArticleDOI
Nucleosome composition regulates the histone H3 tail conformational ensemble and accessibility.
Emma A. Morrison,Emma A. Morrison,Lokesh Baweja,Michael G. Poirier,Jeff Wereszczynski,Catherine A. Musselman,Catherine A. Musselman +6 more
TL;DR: The results indicate that nucleosome composition has the potential to regulate chromatin signaling and ultimately help shape the chromatin landscape.
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.
Journal ArticleDOI
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Journal ArticleDOI
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