Chemistry
Listando 18 trabajos del autor/autora 38
Lista de trabajos en el área Chemistry
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Article
K-DEEP: Protein-Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks
Jimenez, Jose; Skalic, Miha; Martinez-Rosell, Gerard; de Fabritiis, Gianni
JOURNAL OF CHEMICAL INFORMATION AND MODELING
1549-9596 (2018)
DOI /
10.1021/acs.jcim.7b00650
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115
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TorchMD: A Deep Learning Framework for Molecular Simulations
Doerr, Stefan; Majewski, Maciej; Perez, Adria; Kramer, Andreas; Clementi, Cecilia; Noe, Frank; Giorgino, Toni; de Fabritiis, Gianni
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
1549-9618 (2021)
DOI /
10.1021/acs.jctc.0c01343
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109
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Machine Learning of Coarse-Grained Molecular Dynamics Force Fields
Wang, Jiang; Olsson, Simon; Wehmeyer, Christoph; Perez, Adria; Charron, Nicholas E.; de Fabritiis, Gianni; Noe, Frank; Clementi, Cecilia
ACS CENTRAL SCIENCE
2374-7943 (2019)
DOI /
10.1021/acscentsci.8b00913
Gold DOAJ, Green published
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38
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Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling
Plattner, Nuria; Doerr, Stefan; de Fabritiis, Gianni; Noe, Frank
NATURE CHEMISTRY
1755-4330 (2017)
DOI /
10.1038/nchem.2785
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82
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Coarse graining molecular dynamics with graph neural networks
Husic, Brooke E.; Charron, Nicholas E.; Lemm, Dominik; Wang, Jiang; Perez, Adria; Majewski, Maciej; Kramer, Andreas; Chen, Yaoyi; Olsson, Simon; de Fabritiis, Gianni; Noe, Frank; Clementi, Cecilia
JOURNAL OF CHEMICAL PHYSICS
0021-9606 (2020)
DOI /
10.1063/5.0026133
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54
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High-Throughput Automated Preparation and Simulation of Membrane Proteins with HTMD
Doerr, Stefan; Giorgino, Toni; Martinez-Rosell, Gerard; Damas, Joao M.; de Fabritiis, Gianni
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
1549-9618 (2017)
DOI /
10.1021/acs.jctc.7b00480
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38
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Shape-Based Generative Modeling for de Novo Drug Design
Skalic, Miha; Jimenez, Jose; Sabbadin, Davide; de Fabritiis, Gianni
JOURNAL OF CHEMICAL INFORMATION AND MODELING
1549-9596 (2019)
DOI /
10.1021/acs.jcim.8b00706
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27
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A Scalable Molecular Force Field Parameterization Method Based on Density Functional Theory and Quantum-Level Machine Learning
Galvelis, Raimondas; Doerr, Stefan; Damas, Joao M.; Harvey, Matt J.; de Fabritiis, Gianni
JOURNAL OF CHEMICAL INFORMATION AND MODELING
1549-9596 (2019)
DOI /
10.1021/acs.jcim.9b00439
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28
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PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulations
Martinez-Rosell, Gerard; Lovera, Silvia; Sands, Zara A.; de Fabritiis, Gianni
JOURNAL OF CHEMICAL INFORMATION AND MODELING
1549-9596 (2020)
DOI /
10.1021/acs.jcim.9b01209
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31
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PlayMolecule ProteinPrepare: A Web Application for Protein Preparation for Molecular Dynamics Simulations
Martinez-Rosell, Gerard; Giorgino, Toni; de Fabritiis, Gianni
JOURNAL OF CHEMICAL INFORMATION AND MODELING
1549-9596 (2017)
DOI /
10.1021/acs.jcim.7b00190
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16
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Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations
Herrera-Nieto, Pablo; Perez, Adria; de Fabritiis, Gianni
JOURNAL OF CHEMICAL INFORMATION AND MODELING
1549-9596 (2020)
DOI /
10.1021/acs.jcim.0c00381
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9
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DeltaDelta neural networks for lead optimization of small molecule potency
Jimenez-Luna, Jose; Perez-Benito, Laura; Martinez-Rosell, Gerard; Sciabola, Simone; Torella, Rubben; Tresadern, Gary; de Fabritiis, Gianni
CHEMICAL SCIENCE
2041-6520 (2019)
DOI /
10.1039/c9sc04606b
Green published, Gold
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16
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PathwayMap: Molecular Pathway Association with Self-Normalizing Neural Networks
Jimenez, Jose; Sabbadin, Davide; Cuzzolin, Alberto; Martinez-Rosell, Gerard; Gora, Jacob; Manchester, John; Duca, Jose; de Fabritiis, Gianni
JOURNAL OF CHEMICAL INFORMATION AND MODELING
1549-9596 (2019)
DOI /
10.1021/acs.jcim.8b00711
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10
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Molecular-Simulation-Driven Fragment Screening for the Discovery of New CXCL12 Inhibitors
Martinez-Rosell, Gerard; Harvey, Matt J.; de Fabritiis, Gianni
JOURNAL OF CHEMICAL INFORMATION AND MODELING
1549-9596 (2018)
DOI /
10.1021/acs.jcim.7b00625
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7
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SkeleDock: A Web Application for Scaffold Docking in PlayMolecule
Varela-Rial, Alejandro; Majewski, Maciej; Cuzzolin, Alberto; Martinez-Rosell, Gerard; de Fabritiis, Gianni
JOURNAL OF CHEMICAL INFORMATION AND MODELING
1549-9596 (2020)
DOI /
10.1021/acs.jcim.0c00143
Green submitted
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7
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Article
AdaptiveBandit: A Multi-armed Bandit Framework for Adaptive Sampling in Molecular Simulations
Perez, Adria; Herrera-Nieto, Pablo; Doerr, Stefan; de Fabritiis, Gianni
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
1549-9618 (2020)
DOI /
10.1021/acs.jctc.0c00205
Green submitted
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5
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Article
The Aminotriazole Antagonist Cmpd-1 Stabilises a Distinct Inactive State of the Adenosine 2A Receptor
Landin, Erik J. B.; Lovera, Silvia; de Fabritiis, Gianni; Kelm, Sebastian; Mercier, Joel; McMillan, David; Sessions, Richard B.; Taylor, Richard J.; Sands, Zara A.; Joedicke, Lisa; Crump, Matthew P.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
1433-7851 (2019)
DOI /
10.1002/anie.201902852
Green submitted
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1
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Review
Structure based virtual screening: Fast and slow
Varela-Rial, Alejandro; Majewski, Maciej; de Fabritiis, Gianni
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
1759-0876 (2021)
DOI /
10.1002/wcms.1544
