VAriable ResolutIon Algorithms for macroMOLecular Simulation

Project Information

VARIAMOLS

Grant agreement ID: 758588

DOI

10.3030/758588

Project closed

EC signature date 28 September 2017

Start date 1 January 2018

End date 31 December 2022

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 339 351,00

EU contribution

€ 1 339 351,00

Coordinated by

UNIVERSITA DEGLI STUDI DI TRENTO
Italy

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 (19)

Fast, Accurate, and System-Specific Variable-Resolution Modeling of Proteins

Author(s): Raffaele Fiorentini, Thomas Tarenzi, Raffaello Potestio
Published in: JCIM, 2023, ISSN 1520-5142
Publisher: ACS

A journey through mapping space: characterising the statistical and metric properties of reduced representations of macromolecules

Author(s): Roberto Menichetti; Marco Giulini; Raffaello Potestio
Published in: The European Physical Journal B, Issue 1, 2021, ISSN 1434-6028
Publisher: Springer Verlag
DOI: 10.1140/epjb/s10051-021-00205-9

Density-functional-theory approach to the Hamiltonian adaptive resolution simulation method

Author(s): Luis A. Baptista; Ravi C. Dutta; Mauricio Sevilla; Maziar Heidari; Raffaello Potestio; Kurt Kremer; Robinson Cortes-Huerto
Published in: Journal of Physics: Condensed Matter, Issue 1, 2021, ISSN 0953-8984
Publisher: Institute of Physics Publishing
DOI: 10.1088/1361-648x/abed1d

An Information-Theory-Based Approach for Optimal Model Reduction of Biomolecules

Author(s): Marco Giulini, Roberto Menichetti, M. Scott Shell, Raffaello Potestio
Published in: Journal of Chemical Theory and Computation, Issue 16/11, 2020, Page(s) 6795-6813, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.0c00676

Information-theoretical measures identify accurate low-resolution representations of protein configurational space

Author(s): Raffaello Potestio; Roberto Covino; Margherita Mele
Published in: Soft Matter, 2022, ISSN 1744-683X
Publisher: Royal Society of Chemistry
DOI: 10.1039/d2sm00636g

From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules.

Author(s): Marco Giulini; Marco Giulini; Marta Rigoli; Marta Rigoli; Giovanni Mattiotti; Giovanni Mattiotti; Roberto Menichetti; Roberto Menichetti; Thomas Tarenzi; Thomas Tarenzi; Raffaele Fiorentini; Raffaele Fiorentini; Raffaello Potestio; Raffaello Potestio
Published in: Frontiers in Molecular Biosciences, Vol 8 (2021), Issue 1, 2021, ISSN 2296-889X
Publisher: Frontiers Media S.A.
DOI: 10.3389/fmolb.2021.676976

Structural Basis of Mutation-Dependent p53 Tetramerization Deficiency

Author(s): Marta Rigoli, Giovanni Spagnolli, Giulia Lorengo, Paola Monti, Raffaello Potestio, Emiliano Biasini, Alberto Inga
Published in: International Journal of Molecular Sciences, 2022, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23147960

A Deep Graph Network-Enhanced Sampling Approach to Efficiently Explore the Space of Reduced Representations of Proteins.

Author(s): Federico Errica; Marco Giulini; Marco Giulini; Davide Bacciu; Roberto Menichetti; Roberto Menichetti; Alessio Micheli; Raffaello Potestio; Raffaello Potestio
Published in: Frontiers in Molecular Biosciences, Vol 8 (2021), Issue 1, 2021, ISSN 2296-889X
Publisher: Frontiers Media S.A.
DOI: 10.3389/fmolb.2021.637396

Making sense of complex systems through resolution, relevance, and mapping entropy

Author(s): Roi Holtzman, Marco Giulini, Raffaello Potestio
Published in: PRE, 2022, ISSN 2470-0045
Publisher: APS

A deep learning approach to the structural analysis of proteins

Author(s): Marco Giulini, Raffaello Potestio
Published in: Interface Focus, Issue 9/3, 2019, Page(s) 20190003, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0003

Optimal Coarse-Grained Site Selection in Elastic Network Models of Biomolecules

Author(s): Patrick Diggins, Changjiang Liu, Markus Deserno, Raffaello Potestio
Published in: Journal of Chemical Theory and Computation, Issue 15/1, 2018, Page(s) 648-664, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.8b00654

Open-Boundary Molecular Mechanics/Coarse-Grained Framework for Simulations of Low-Resolution G-Protein-Coupled Receptor–Ligand Complexes

Author(s): Thomas Tarenzi, Vania Calandrini, Raffaello Potestio, Paolo Carloni
Published in: Journal of Chemical Theory and Computation, Issue 15/3, 2019, Page(s) 2101-2109, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.9b00040

Envisioning data sharing for the biocomputing community

Author(s): Enrico Riccardi, Sergio Pantano, Raffaello Potestio
Published in: Interface Focus, Issue 9/3, 2019, Page(s) 20190005, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0005

Multi-resolution simulations of intracellular processes

Author(s): Radek Erban, Sarah Harris, Raffaello Potestio
Published in: Interface Focus, Issue 9/3, 2019, Page(s) 20190028, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0028

Open-boundary Hamiltonian adaptive resolution. From grand canonical to non-equilibrium molecular dynamics simulations

Author(s): Maziar Heidari, Kurt Kremer, Ramin Golestanian, Raffaello Potestio, Robinson Cortes-Huerto
Published in: The Journal of Chemical Physics, Issue 152/19, 2020, Page(s) 194104, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/1.5143268

Ligand‐protein interactions in lysozyme investigated through a dual‐resolution model

Author(s): Raffaele Fiorentini, Kurt Kremer, Raffaello Potestio
Published in: Proteins: Structure, Function, and Bioinformatics, 2020, ISSN 0887-3585
Publisher: Wiley-Liss Inc
DOI: 10.1002/prot.25954

Membrane binding of pore-forming γ-hemolysin components studied at different lipid compositions

Author(s): Thomas Tarenzi, Gianluca Lattanzi, Raffaello Potestio
Published in: Biochimica et Biophysica Acta (BBA) - Biomembranes, 2022, ISSN 0005-2736
Publisher: Elsevier BV
DOI: 10.1016/j.bbamem.2022.183970

Communication pathways bridge local and global conformations in an IgG4 antibody.

Author(s): Thomas Tarenzi; Marta Rigoli; Raffaello Potestio
Published in: Scientific Reports, Vol 11, Iss 1, Pp 1-12 (2021), Issue 1, 2021, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-02323-x

In Search of a Dynamical Vocabulary: A Pipeline to Construct a Basis of Shared Traits in Large-Scale Motions of Proteins

Author(s): Thomas Tarenzi, Marta Rigoli, Giovanni Mattiotti, Raffaello Potestio
Published in: Applied Sciences, 2022, ISSN 2076-3417
Publisher: MDPI
DOI: 10.3390/app12147157