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PhD Thesis - Computational Science

Pérez A. Learning How to Simulate: applying machine learning methods to improve molecular dynamics simulations. Universitat Pompeu Fabra. January, 27th 2022. Thesis Director: De Fabritiis G.

2022

Original articles in indexed journals - Computational Science

Varela-Rial A, Maryanow I, Majewski M, Doerr S, Schapin N, Jiménez-Luna J, De Fabritiis G. PlayMolecule Glimpse: Understanding Protein-Ligand Property Predictions with Interpretable Neural Networks. J Chem Inf Model, 2022; 62(2): 225-231 . PMID: 34978201 . DOI: 10.1021/acs.jcim.1c00691.

2022

Original articles in indexed journals - Computational Science

Olehnovics E, Yin JQ, Perez A, De Fabritiis G, Bonomo RA, Bhowmik D, Haider S. The Role of Hydrophobic Nodes in the Dynamics of Class A β-Lactamases. Front Microbiol, 2021; 12: 72099 DOI: 10.3389/fmicb.2021.720991.

2021

Original articles in indexed journals - Computational Science

Varela-Rial A, Majewski M, De Fabritiis G. Structure based virtual screening: Fast and slow. Wiley Interdisciplinary Reviews-Computational Molecular Science, 2021; e1544 DOI: 10.1002/wcms.1544.

2021

Original articles in indexed journals - Computational Science

Doerr S, Majewski M, Pérez A, Krämer A, Clementi C, Noe F, Giorgino T, De Fabritiis G. TorchMD: A Deep Learning Framework for Molecular Simulations. J Chem Theory Comput, 2021; 13;17(4): 2355-2363. PMID: 33729795 . DOI: 10.1021/acs.jctc.0c01343.

2021

Original articles in indexed journals - Computational Science

Merz KM Jr, De Fabritiis G, Wei GW. Generative Models for Molecular Design. J Chem Inf Model, 2020; 60(12): 5635-5636. PMID: 33378853 . DOI: 10.1021/acs.jcim.0c01388.

2020

Original articles in indexed journals - Computational Science

Husic BE, Charron NE, Lemm D, Wang J, Pérez A, Majewski M, Krämer A, Chen Y, Olsson S, de Fabritiis G, Noé F, Clementi C. Coarse graining molecular dynamics with graph neural networks. J Chem Phys, 2020; 153(19): 194101. PMID: 33218238 . DOI: 10.1063/5.0026133.

2020

Original articles in indexed journals - Computational Science

Herrera-Nieto P, Pérez A, De Fabritiis G. Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations. J Chem Inf Model, 2020; 60:10; 5003-5010. PMID: 32786705 . DOI: 10.1021/acs.jcim.0c00381.

2020

Original articles in indexed journals - Computational Science

Pérez A, Herrera-Nieto P, Doerr S, De Fabritiis G. AdaptiveBandit: A multi-armed bandit framework for adaptive sampling in molecular simulations. J Chem Theory Comput, 2020; 16(7): 4685-4693. PMID: 32539384 . DOI: 10.1021/acs.jctc.0c00205.

2020



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