Zobrazeno 1 - 10
of 61
pro vyhledávání: '"Simon Bray"'
Publikováno v:
Journal of Cheminformatics, Vol 14, Iss 1, Pp 1-13 (2022)
Abstract We present several workflows for protein-ligand docking and free energy calculation for use in the workflow management system Galaxy. The workflows are composed of several widely used open-source tools, including rDock and GROMACS, and can b
Externí odkaz:
https://doaj.org/article/666d8e3c206b4581b1baea162288ff09
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-8 (2020)
Protein-ligand unbinding processes are out of reach for atomistic simulations due to time-scale involved. Here the authors demonstrate an approach relying on dissipation-corrected targeted molecular dynamics that enables to provide binding and unbind
Externí odkaz:
https://doaj.org/article/74993a4b0fe84c8f921372814fbda8bb
Autor:
Qiang Gu, Anup Kumar, Simon Bray, Allison Creason, Alireza Khanteymoori, Vahid Jalili, Björn Grüning, Jeremy Goecks
Publikováno v:
PLoS Computational Biology, Vol 17, Iss 6, p e1009014 (2021)
Supervised machine learning is an essential but difficult to use approach in biomedical data analysis. The Galaxy-ML toolkit (https://galaxyproject.org/community/machine-learning/) makes supervised machine learning more accessible to biomedical scien
Externí odkaz:
https://doaj.org/article/cc0c9acee42140dc8b0a5f096e5da22d
Publikováno v:
Environment International, Vol 149, Iss , Pp 106362- (2021)
Trace elements (TEs) frequently contaminate coastal marine sediments with many included in priority chemical lists or control legislation. These, improved waste treatment and increased recycling have fostered the belief that TE pollution is declining
Externí odkaz:
https://doaj.org/article/b5816bc2e7904cefb1bafbf68951615e
Publikováno v:
Data in Brief, Vol 35, Iss , Pp 106901- (2021)
The present Data In Brief methodological paper details the acquisition, mining and pre-processing of elemental concentration data in marine sediments (coastal and open sea) of Southern England, presented and discussed in the co-submitted Environment
Externí odkaz:
https://doaj.org/article/192d68ad39364da0ba61cff275b0264b
Autor:
Simon Bray, John Chilton, Matthias Bernt, Nicola Soranzo, Marius van den Beek, Bérénice Batut, Helena Rasche, Martin Čech, Peter J.A. Cock, Björn Grüning, Anton Nekrutenko
Publikováno v:
Genome Research, 33(3), 261-268. Cold Spring Harbor Laboratory Press
There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For more than a decade, the Galaxy Project has been providing computational infrastructure and a unified user interface fo
Autor:
Simon Bray, Matthias Bernt, Nicola Soranzo, Marius van den Beek, Bérénice Batut, Helena Rasche, Martin Čech, Peter Cock, Anton Nekrutenko, Björn Grüning, John Chilton
There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For over a decade, the Galaxy Project has been providing computational infrastructure and a unified user interface for the
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::9a3847a9efdd0aa893ecac98aa8ed4a5
https://doi.org/10.1101/2022.03.13.483965
https://doi.org/10.1101/2022.03.13.483965
We present two methods to reveal protein-ligand unbinding mechanisms in biased unbinding simulations by clustering trajectories into ensembles representing unbinding paths. The first approach is based on a contact principal component analysis for red
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e842e7c586d18a566b25cdcbcf706d59
Autor:
Tim Dudgeon, Frank Von Delft, Simon Bray, Rachael Elaine Skyner, Rolf Backofen, Björn Grüning
Publikováno v:
Journal of cheminformatics. 14(1)
We present several workflows for protein-ligand docking and free energy calculation for use in the workflow management system Galaxy. The workflows are composed of several widely used open-source tools, including rDock and GROMACS, and can be execute
Autor:
Björn Grüning, Allison L. Creason, Jeremy Goecks, Anup Kumar, Alireza Khanteymoori, Vahid Jalili, Simon Bray, Qiang Gu
Publikováno v:
PLoS Computational Biology, Vol 17, Iss 6, p e1009014 (2021)
PLoS Computational Biology
PLoS Computational Biology
Supervised machine learning is an essential but difficult to use approach in biomedical data analysis. The Galaxy-ML toolkit (https://galaxyproject.org/community/machine-learning/) makes supervised machine learning more accessible to biomedical scien