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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Structure-based identification of potential SARS-CoV-2 main protease inhibitors.
Shama Khan,Zeynab Fakhar,Afzal Hussain,Aijaz Ahmad,Aijaz Ahmad,Deeba Shamim Jairajpuri,Mohamed F. Alajmi,Imtaiyaz Hassan +7 more
TL;DR: Five potential inhibitors of the main protease (Mpro) enzyme of SARS-CoV-2 Mpro are identified by using structure-based drug design, pharmacophore modeling, and virtual high throughput drug screening combined with docking and all-atom molecular dynamics simulation approach.
Journal ArticleDOI
Experimental and computational insights on the recognition mechanism between the estrogen receptor α with bisphenol compounds
TL;DR: Structural perturbations that are induced by the three compounds were confirmed to reduce the recruitment potency of co-activators more than other BPs based on calculations of binding free energies, which is in line with observed experimental transcriptional activities.
Journal ArticleDOI
Activation of the α2B adrenoceptor by the sedative sympatholytic dexmedetomidine.
Daopeng Yuan,Zhongmin Liu,Jonas Kaindl,Shoji Maeda,Jiawei Zhao,Xiaoou Sun,Jun Xu,Peter Gmeiner,Hong-Wei Wang,Brian K. Kobilka +9 more
TL;DR: A cryo-EM structure of the GPCR α2B adrenergic receptor (α2BAR) in complex with the selective agonist dexmedetomidine and the G protein Go suggests a mechanism of selective activation and provides insights into G-protein coupling activity.
Journal ArticleDOI
Foldamer-based ultrapermeable and highly selective artificial water channels that exclude protons
Arundhati Roy,Jie Shen,Himanshu Joshi,Woochul Song,Yu-Ming Tu,Ratul Chowdhury,Ruijuan Ye,Ning Li,Changliang Ren,Manish Kumar,Aleksei Aksimentiev,Huaqiang Zeng,Huaqiang Zeng +12 more
TL;DR: A class of biomimetic, helically folded pore-forming polymeric foldamers can serve as long-sought-after highly selective ultrafast water-conducting channels exceeding those of aquaporins with high water-over-monovalent-ion transport selectivity conferred by the modularly tunable hydrophobicity of the interior pore surface.
Journal ArticleDOI
Computational approach and electrochemical measurements for protein detection with MIP-based sensor.
Zouhour Mazouz,Meriem Mokni,Najla Fourati,Chouki Zerrouki,Florent Barbault,Mahamadou Seydou,Rafik Kalfat,Nourdin Yaakoubi,Asma Omezzine,Ali Bouslema,Ali Othmane +10 more
TL;DR: Electrochemical sensors based on polypyrrol (PPy) molecular imprinted polymers (MIP) for proteins detection at low concentrations with high selectivity and reproducibility and PSA concentration values directly measured in 35 human serum samples were found closely correlated to those measured by the ELISA technique.
References
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