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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Understanding the co-loading and releasing of doxorubicin and paclitaxel using chitosan functionalized single-walled carbon nanotubes by molecular dynamics simulations
Konda Reddy Karnati,Yixuan Wang +1 more
TL;DR: The results indicate that the co-loading of DOX and PTX onto the pristine SWCNT is exothermic and spontaneous, and the encapsulation of anticancer drugs may also play a very important role and should be considered in the drug delivery.
Journal ArticleDOI
Ligand recognition and allosteric regulation of DRD1-Gs signaling complexes
Peng Xiao,Wei Yan,Lu Gou,Ya Ni Zhong,Liangliang Kong,Chao Wu,Xin Wen,Yuan Yuan,Sheng Cao,Changxiu Qu,Xin Yang,Chuan Cheng Yang,Anjie Xia,Zhenquan Hu,Qianqian Zhang,Yong Hao He,Dao Lai Zhang,Chao Zhang,Gui Hua Hou,Huanxiang Liu,Lizhe Zhu,Ping Fu,Shengyong Yang,Daniel M. Rosenbaum,Jin-Peng Sun,Jin-Peng Sun,Yang Du,Lei Zhang,Xiao Yu,Zhenhua Shao +29 more
TL;DR: In this paper, the D1 receptor (DRD1) coupled to Gs heterotrimer in complex with three catechol-based agonists, a non-catechol agonist, and a positive allosteric modulator for endogenous dopamine.
Journal ArticleDOI
Structural mechanisms of selectivity and gating in anion channelrhodopsins
Hideaki E. Kato,Yoon Seok Kim,Joseph M. Paggi,Kathryn E. Evans,Kathryn E. Evans,William E. Allen,William E. Allen,Claire E. Richardson,Keiichi Inoue,Keiichi Inoue,Shota Ito,Charu Ramakrishnan,Charu Ramakrishnan,Lief E. Fenno,Lief E. Fenno,Keitaro Yamashita,Daniel Hilger,Soo Yeun Lee,Soo Yeun Lee,Andre Berndt,Andre Berndt,Kang Shen,Hideki Kandori,Ron O. Dror,Brian K. Kobilka,Karl Deisseroth,Karl Deisseroth +26 more
TL;DR: Crystal structures and molecular simulations of the designed anion-conducting channelrhodopsin iC++ provide molecular insights that enable structure-based design of channel rhodopsins with desirable properties for use as optogenetic tools.
Journal ArticleDOI
Selective recognition of c-MYC Pu22 G-quadruplex by a fluorescent probe.
Qianqian Zhai,Chao Gao,Jieqin Ding,Yashu Zhang,Barira Islam,Wenxian Lan,Haitao Hou,Hua Deng,Li Jun,Zhe Hu,Hany I. Mohamed,Hany I. Mohamed,Shengzhen Xu,Chunyang Cao,Shozeb Haider,Dengguo Wei +15 more
TL;DR: Both the single stacking state and the dynamic recognition process are crucial for designing fluorescent probes or ligands with high selectivity for a specific G-quadruplex structure, implies this study implies.
Journal ArticleDOI
PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations
Maximilian Scheurer,Maximilian Scheurer,Maximilian Scheurer,Peter J. Rodenkirch,Marc Siggel,Rafael C. Bernardi,Klaus Schulten,Emad Tajkhorshid,Till Rudack,Till Rudack +9 more
TL;DR: PyContact, an easy-to-use, highly flexible, and intuitive graphical user interface-based application, designed to provide a toolkit to investigate biomolecular interactions in MD trajectories, analyzes and visualizes the noncovalent interactions underlying the ion permeation pathway of the human P2X3 receptor.
References
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VMD: Visual molecular dynamics
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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.
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Journal ArticleDOI
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.