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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Novel Peptide Inhibitors for Lactate Dehydrogenase A (LDHA): A Survey to Inhibit LDHA Activity via Disruption of Protein-Protein Interaction.
TL;DR: In silico methods to design inhibitory peptides for lactate dehydrogenase through the disturbance in tetramerization, the results showed that the designed peptides which mimic the N-terminal arm of the enzyme can successfully target the C- terminal domain and interrupt the bona fide form of the enzymes subunits.
Journal ArticleDOI
AIMMS suite: a web server dedicated for prediction of drug resistance on protein mutation.
Feng-Xu Wu,Fan Wang,Jing-Fang Yang,Wen Jiang,Meng-Yao Wang,Chen-Yang Jia,Ge-Fei Hao,Guang-Fu Yang,Guang-Fu Yang +8 more
TL;DR: Auto In Silico Macromolecular Mutation Scanning (AIMMS), a web server for computer-aided de novo drug resistance prediction for any ligand-protein systems, which can qualitatively estimate the free energy consequences of any mutations through a fast mutagenesis scanning calculation based on a single molecular dynamics trajectory.
Journal ArticleDOI
Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge
TL;DR: The correlation between experimental and computational free energy of binding ranks as one of the highest with respect to other entries in the challenge, and the large MUE for the best performing model highlights systematic errors.
Journal ArticleDOI
Partially inserted nascent chain unzips the lateral gate of the Sec translocon.
Lukas Kater,Benedikt Frieg,Otto Berninghausen,Holger Gohlke,Holger Gohlke,Roland Beckmann,Alexej Kedrov,Alexej Kedrov +7 more
TL;DR: A cryo‐electron microscopy‐based structure and biochemical data suggest that the partially inserted nascent chain remains highly flexible until it acquires the transmembrane topology.
Journal ArticleDOI
Interfering with HuR-RNA Interaction: Design, Synthesis and Biological Characterization of Tanshinone Mimics as Novel, Effective HuR Inhibitors.
Leonardo Manzoni,Chiara Zucal,Danilo Di Maio,Vito Giuseppe D'Agostino,Natthakan Thongon,Isabelle Bonomo,Preet Lal,Marco Miceli,Vanessa Baj,Marta Brambilla,Linda Cerofolini,Saioa R. Elezgarai,Emiliano Biasini,Emiliano Biasini,Claudio Luchinat,Ettore Novellino,Marco Fragai,Luciana Marinelli,Alessandro Provenzani,Pierfausto Seneci +19 more
TL;DR: Inspired by DHTS structure, an array of ortho-quinones (tanshinone mimics) were designed and synthesized using a function-oriented synthetic approach and turned out to be more effective than 1, showing a nanomolar Ki and disrupting HuR binding to RNA in cells.
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
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Journal ArticleDOI
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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.
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Journal ArticleDOI
General definition of ring puckering coordinates
Dieter Cremer,John A. Pople +1 more
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