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 organization of a major neuronal G protein regulator, the RGS7-Gβ5-R7BP complex.
Dipak N. Patil,Erumbi S. Rangarajan,Scott J. Novick,Bruce D. Pascal,Douglas J. Kojetin,Patrick R. Griffin,Tina Izard,Kirill A. Martemyanov +7 more
TL;DR: A crystal structure and dynamics analyses of the multisubunit complex of RGS7, a major regulator of neuronal signaling with key roles in controlling a number of drug target GPCRs and links to neuropsychiatric disease, metabolism, and cancer are reported.
Journal ArticleDOI
Single H5N1 influenza A neuraminidase mutation develops resistance to oseltamivir due to distorted conformational and drug binding landscape: multiple molecular dynamics analyses
TL;DR: In this article, a comparative study on the wild type and I117V mutant was conducted to understand the origin of resistance at the molecular level using a wide range of post-dynamics analytical tools.
Journal ArticleDOI
Topological and electrostatic properties of diclofenac molecule as a non-steroidal anti-inflammatory drug: An experimental and theoretical study
R. Niranjana Devi,A. David Stephen,P. Justin,Kandasamy Saravanan,Piero Macchi,Piero Macchi,Christian Jelsch +6 more
TL;DR: In this paper, the electron density of Diclofenac was analyzed using high-resolution X-ray diffraction data at 110'K and theoretical calculations, and the topological properties of the dimer interactions in both the crystal phase and human transthyretin protein environment were identified.
Journal ArticleDOI
Immunogenic SARS-CoV-2 epitopes: In silico study towards better understanding of COVID-19 disease—paving the way for vaccine development
TL;DR: Using in silico analyses, it is shown that human major histocompatibility complex (MHC) class I cell-surface molecules vary in their capacity for binding different SARS-CoV-2-derived epitopes, and a structural explanation for the binding of Sars- CoV- 2-epitopes to MHC molecules is given.
Journal ArticleDOI
The potential effects of clinical antidiabetic agents on SARS-CoV-2.
Hua Qu,Yi Zheng,Yuren Wang,Hongwei Li,Xiufei Liu,Xin Xiong,Linlin Zhang,Jing Gu,Gangyi Yang,Zhiming Zhu,Hongting Zheng,Qin Ouyang +11 more
TL;DR: It is still unclear whether diabetic treatment principles can be used for the treatment of COVID‐19, but it is notable that a substantial proportion of patients with sever COvid‐19 have coexisting diabetic conditions, indicating the progression and outcome of CO VID‐19 may relate to diabetes.
References
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VMD: Visual molecular dynamics
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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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