Computational Microscope on Molecular Binding: from atom to cell membrane scale

Project Information

CoMMBi

Grant agreement ID: 101001784

DOI 10.3030/101001784

EC signature date 25 May 2021

Start date 1 September 2021

End date 31 August 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 1 999 497,00

EU contribution € 1 999 497,00

Coordinated by

UNIVERSITA DELLA SVIZZERA ITALIANA
Switzerland

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (13)

Drug Repurposing on G Protein-Coupled Receptors Using a Computational Profiling Approach

Author(s): Alessandra de Felice, Simone Aureli, Vittorio Limongelli
Published in: Frontiers in Molecular Biosciences, 2021, ISSN 2296-889X
Publisher: Frontiers Media SA
DOI: 10.3389/fmolb.2021.673053

Expanding the Library of 1,2,4-Oxadiazole Derivatives: Discovery of New Farnesoid X Receptor (FXR) Antagonists/Pregnane X Receptor (PXR) Agonists

Author(s): Claudia Finamore, Carmen Festa, Bianca Fiorillo, Francesco Saverio Di Leva, Rosalinda Roselli, Silvia Marchianò, Michele Biagioli, Lucio Spinelli, Stefano Fiorucci,Vittorio Limongelli, Angela Zampella, Simona De Marino
Published in: Molecules, 2023, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules28062840

Uracil/H+ Symport by FurE Refines Aspects of the Rocking-bundle Mechanism of APC-type Transporters

Author(s): Iliana Zantza, Yiannis Pyrris, Stefano Raniolo, Georgia F. Papadaki, George Lambrinidis, Vittorio Limongelli, George Diallinas, Emmanuel Mikros
Published in: Journal of Molecular Biology, 2023, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2023.168226

Structural Basis for Developing Multitarget Compounds Acting on Cysteinyl Leukotriene Receptor 1 and G-Protein-Coupled Bile Acid Receptor 1

Author(s): Bianca Fiorillo; Valentina Sepe; Paolo Conflitti; Rosalinda Roselli; Michele Biagioli; Silvia Marchianò; Pasquale De Luca; Giuliana Baronissi; Pasquale Rapacciuolo; Chiara Cassiano; Bruno Catalanotti; Angela Zampella; Vittorio Limongelli; Vittorio Limongelli; Stefano Fiorucci
Published in: JOURNAL OF MEDICINAL CHEMISTRY, Issue 1, 2021, ISSN 0022-2623
Publisher: American Chemical Society
DOI: 10.1021/acs.jmedchem.1c01078

Discovery of a Novel Class of Dual GPBAR1 Agonists–RORγt Inverse Agonists for the Treatment of IL-17-Mediated Disorders

Author(s): Bianca Fiorillo; Rosalinda Roselli; Claudia Finamore; Michele Biagioli; Cristina di Giorgio; Martina Bordoni; Paolo Conflitti; Silvia Marchianò; Rachele Bellini; Pasquale Rapacciuolo; Chiara Cassiano; Vittorio Limongelli; Valentina Sepe; Bruno Catalanotti; Stefano Fiorucci; Angela Zampella
Published in: ACS Omega, Issue 1, 2023, ISSN 2470-1343
Publisher: American Chemical Society
DOI: 10.1021/acsomega.2c07907

Transferring chemical and energetic knowledge between molecular systems with machine learning

Author(s): Sajjad Heydari, Stefano Raniolo, Lorenzo Livi, Vittorio Limongelli
Published in: Communications Chemistry, 2023, ISSN 2399-3669
Publisher: Nature Publishing Group
DOI: 10.1038/s42004-022-00790-5

Improving Small-Molecule Force Field Parameters in Ligand Binding Studies

Author(s): Stefano Raniolo, Vittorio Limongelli
Published in: Frontiers in Molecular Biosciences, 2021, ISSN 2296-889X
Publisher: Frontiers Media SA
DOI: 10.3389/fmolb.2021.760283

Phosphorylation of FAM134C by CK2 controls starvation-induced ER-phagy

Author(s): GIORGIA DI LORENZO, FRANCESCOPAOLO IAVARONE, MARIANNA MADDALUNO, ANA BELÉN PLATA-GÓMEZ, SIMONE AURELI, CAMILA PAZ QUEZADA MEZA, LAURA CINQUE, ALESSANDRO PALMA, ALESSIO REGGIO, CARMINE CIRILLO, FRANCESCA SACCO, ALEXANDRA STOLZ, GENNARO NAPOLITANO, ORIANO MARIN, LORENZO A. PINNA, MARIA RUZZENE, VITTORIO LIMONGELLI, ALEJO EFEYAN, PAOLO GRUMATI, CARMINE SETTEMBRE
Published in: SCIENCE ADVANCES, 2022, ISSN 2375-2548
Publisher: American Association for the Advancement of Science
DOI: 10.1126/sciadv.abo1215

Discovery of Bile Acid Derivatives as Potent ACE2 Activators by Virtual Screening and Essential Dynamics

Author(s): Bianca Fiorillo; Silvia Marchianò; Federica Moraca; Valentina Sepe; Adriana Carino; Pasquale Rapacciuolo; Michele Biagioli; Vittorio Limongelli; Angela Zampella; Bruno Catalanotti; Stefano Fiorucci
Published in: Journal of Chemical Information and Modeling, Issue 1, 2021, ISSN 1549-960X
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.1c01126

Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness

Author(s): Paolo Conflitti, Stefano Raniolo, Vittorio Limongelli
Published in: Journal of Chemical Theory and Computation, 2023, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.3c00641

Discovery of a Potent and Orally Active Dual GPBAR1/CysLT1R Modulator for the Treatment of Metabolic Fatty Liver Disease

Author(s): Stefano Fiorucci, Pasquale Rapacciuolo, Bianca Fiorillo, Rosalinda Roselli, Silvia Marchianò, Cristina Di Giorgio, Martina Bordoni, Rachele Bellini, Chiara Cassiano, Paolo Conflitti, Bruno Catalanotti, Vittorio Limongelli, Valentina Sepe, Michele Biagioli, Angela Zampella
Published in: Frontiers in Pharmacology, 2022, ISSN 1663-9812
Publisher: Frontiers Media S.A.
DOI: 10.3389/fphar.2022.858137

Structural basis of dimerization of chemokine receptors CCR5 and CXCR4

Author(s): Daniele di Marino, Paolo Conflitti, Stefano Motta, Vittorio Limongelli
Published in: Nature Communications, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-42082-z

Conformational plasticity and allosteric communication networks explain Shelterin protein TPP1 binding to human telomerase

Author(s): Simone Aureli, Vince Bart Cardenas, Stefano Raniolo, Vittorio Limongelli
Published in: Communications Chemistry, Issue 1, 2023, ISSN 2399-3669
Publisher: Nature Portfolio
DOI: 10.1038/s42004-023-01040-y

Other (1)

HEroBM: a deep equivariant graph neural network for universal backmapping from coarse-grained to all-atom representations

Author(s): Daniele Angioletti, Stefano Raniolo, Vittorio Limongelli
Published in: arXiv, 2024
Publisher: Cornell Tech
DOI: 10.48550/arxiv.2404.16911

Non-peer reviewed articles (1)

Minute-timescale free-energy calculations reveal a pseudo-active state in the adenosine A2A receptor activation mechanism

Author(s): Vincenzo Maria D’Amore, Paolo Conflitti, Luciana Marinelli, Vittorio Limongelli
Published in: Chem, 2024, ISSN 2451-9308
Publisher: Cell Press
DOI: 10.1016/j.chempr.2024.08.004