BioExcel-2 D2.7 – Final release of demonstration workflows

Autor: Adam Hospital, Genís Bayarri, Stian Soiland- Reyes, Douglas Lowe, Josep Lluís Gelpí, Pau Andrio, Daniele Lezzi, Jorge Ejarque, Sarah Butcher, Ania Niewielska, Alberto Eusebi, Esther Sala, Aristarc Surinach, Martí Municoy, Rosa Maria Badia, Rodrigo Vargas, Alexandre Bonvin

This deliverable presents the final release of demonstration workflows for the BioExcel-2 project, including a wrap-up of all the work done for the BioBB library, its associated workflows, and a final analysis of the milestones achieved from the init

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::92d5f4016c8cff24b7fe30a2d40d696d

High-throughput prediction of the impact of genetic variability on drug sensitivity and resistance patterns for clinically relevant epidermal growth factor receptor mutations from atomistic simulations

Autor: Aristarc Suriñach, Adam Hospital, Yvonne Westermaier, Luis Jordà, Sergi Orozco-Ruiz, Daniel Beltrán, Francesco Colizzi, Pau Andrio, Robert Soliva, Martí Municoy, Josep Lluís Gelpí, Modesto Orozco

14 pages, 6 figures, 1 table, supporting information https://pubs.acs.org/doi/10.1021/acs.jcim.2c01344.-- The code for this work is available at https://github.com/bioexcel/biobb_hpc_workflows/tree/condapack. MD simulations are available from our MDp

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6ac9fde04c21be9e4c703907677b4022
https://hdl.handle.net/2117/383723

PELE-MSM: A Monte Carlo Based Protocol for the Estimation of Absolute Binding Free Energies

Autor: Christian Tyrchan, Robert Soliva, Martí Municoy, Oriol Gracia Carmona, Martin J. Packer, Daniel Soler, Joan Gilabert, Victor Guallar, Anders Hogner, Samantha Jayne Hughes, Christoph Grebner, Daniel Lecina

Publikováno v: Journal of Chemical Theory and Computation. 15:6243-6253

In this study, we present a fully automatic platform based on our Monte Carlo algorithm, the Protein Energy Landscape Exploration method (PELE), for the estimation of absolute protein-ligand binding free energies, one of the most significant challeng

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3b0432aa69aaf988f74cc130d1d7a632
https://doi.org/10.1021/acs.jctc.9b00753

aquaPELE: A Monte Carlo-based algorithm to sample the effects of buried water molecules in proteins

Autor: Alberto Soutullo, Victor Guallar, Sergi Roda, Daniel Soler, Martí Municoy

Publikováno v: UPCommons. Portal del coneixement obert de la UPC
Universitat Politècnica de Catalunya (UPC)

Water is frequently found inside proteins, carrying out important roles in catalytic reactions or molecular recognition tasks. Therefore, computational models that aim to study protein–ligand interactions usually have to include water effects throu

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bce731eada40d05d2adf51cae9a3de70

Selective synthesis of 4-hydroxyisophorone and 4-ketoisophorone by fungal peroxygenases

Autor: José C. del Río, Ángel T. Martínez, Carmen Aranda, Jan Kiebist, René Ullrich, Martin Hofrichter, Martí Municoy, Ana Gutiérrez, Victor Guallar, Katrin Scheibner

Publikováno v: UPCommons. Portal del coneixement obert de la UPC
Universitat Politècnica de Catalunya (UPC)
Recercat. Dipósit de la Recerca de Catalunya
instname
Digital.CSIC. Repositorio Institucional del CSIC
Catalysis Science & Technology

8 páginas.-- 4 figuras.-- 4 tablas.-- 43 referencias.-- Supporting information http://www.rsc.org/suppdata/c8/cy/c8cy02114g/c8cy02114g1.pdf
The recently discovered unspecific peroxygenases (UPOs) from the ascomycetes Chaetomium globosum and Hum

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8fe5bef23a958e6ab2e0eee46c1bc2e9