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- Universitat Pompeu FabraES29 papers
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6 papers · 1 filter
AMARO: All Heavy-Atom Transferable Neural Network Potentials of Protein Thermodynamics
Antonio Mirarchi, Raul P. Pelaez, Guillem Simeon +1
All-atom molecular simulations offer detailed insights into macromolecular phenomena, but their substantial computational cost hinders the exploration of complex biological process…
mdCATH: A Large-Scale MD Dataset for Data-Driven Computational Biophysics
Antonio Mirarchi, Toni Giorgino, Gianni De Fabritiis
Recent advancements in protein structure determination are revolutionizing our understanding of proteins. Still, a significant gap remains in the availability of comprehensive data…
PlayMolecule Viewer: a toolkit for the visualization of molecules and other data
Mariona Torrens-Fontanals, Panagiotis Tourlas, Stefan Doerr +1
PlayMolecule Viewer is a web-based data visualization toolkit designed to streamline the exploration of data resulting from structural bioinformatics or computer-aided drug design…
Machine Learning Coarse-Grained Potentials of Protein Thermodynamics
Maciej Majewski, Adrià Pérez, Philipp Thölke +7
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships t…
Simulations meet Machine Learning in Structural Biology
Adrià Pérez, Gerard Martínez-Rosell, Gianni De Fabritiis
Classical molecular dynamics (MD) simulations will be able to reach sampling in the second timescale within five years, producing petabytes of simulation data at current force fiel…
RNAiFold2T: Constraint Programming design of thermo-IRES switches
Juan Antonio Garcia-Martin, Ivan Dotu, Javier Fernandez-Chamorro +4
Motivation: RNA thermometers (RNATs) are cis-regulatory ele- ments that change secondary structure upon temperature shift. Often involved in the regulation of heat shock, cold shoc…