VAriable ResolutIon Algorithms for macroMOLecular Simulation

Información del proyecto

VARIAMOLS

Identificador del acuerdo de subvención: 758588

DOI

10.3030/758588

Proyecto cerrado

Fecha de la firma de la CE 28 Septiembre 2017

Fecha de inicio 1 Enero 2018

Fecha de finalización 31 Diciembre 2022

Financiado con arreglo a

• EXCELLENT SCIENCE - European Research Council (ERC)

Coste total

€ 1 339 351,00

Aportación de la UE

€ 1 339 351,00

Coordinado por

UNIVERSITA DEGLI STUDI DI TRENTO
Italy

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Publicaciones

Peer reviewed articles (19)

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

Autores: Raffaele Fiorentini, Thomas Tarenzi, Raffaello Potestio
Publicado en: JCIM, 2023, ISSN 1520-5142
Editor: ACS

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

Autores: Roberto Menichetti; Marco Giulini; Raffaello Potestio
Publicado en: The European Physical Journal B, Edición 1, 2021, ISSN 1434-6028
Editor: Springer Verlag
DOI: 10.1140/epjb/s10051-021-00205-9

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

Autores: Luis A. Baptista; Ravi C. Dutta; Mauricio Sevilla; Maziar Heidari; Raffaello Potestio; Kurt Kremer; Robinson Cortes-Huerto
Publicado en: Journal of Physics: Condensed Matter, Edición 1, 2021, ISSN 0953-8984
Editor: Institute of Physics Publishing
DOI: 10.1088/1361-648x/abed1d

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

Autores: Marco Giulini, Roberto Menichetti, M. Scott Shell, Raffaello Potestio
Publicado en: Journal of Chemical Theory and Computation, Edición 16/11, 2020, Página(s) 6795-6813, ISSN 1549-9618
Editor: American Chemical Society
DOI: 10.1021/acs.jctc.0c00676

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

Autores: Raffaello Potestio; Roberto Covino; Margherita Mele
Publicado en: Soft Matter, 2022, ISSN 1744-683X
Editor: 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.

Autores: 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
Publicado en: Frontiers in Molecular Biosciences, Vol 8 (2021), Edición 1, 2021, ISSN 2296-889X
Editor: Frontiers Media S.A.
DOI: 10.3389/fmolb.2021.676976

Structural Basis of Mutation-Dependent p53 Tetramerization Deficiency

Autores: Marta Rigoli, Giovanni Spagnolli, Giulia Lorengo, Paola Monti, Raffaello Potestio, Emiliano Biasini, Alberto Inga
Publicado en: International Journal of Molecular Sciences, 2022, ISSN 1422-0067
Editor: 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.

Autores: Federico Errica; Marco Giulini; Marco Giulini; Davide Bacciu; Roberto Menichetti; Roberto Menichetti; Alessio Micheli; Raffaello Potestio; Raffaello Potestio
Publicado en: Frontiers in Molecular Biosciences, Vol 8 (2021), Edición 1, 2021, ISSN 2296-889X
Editor: Frontiers Media S.A.
DOI: 10.3389/fmolb.2021.637396

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

Autores: Roi Holtzman, Marco Giulini, Raffaello Potestio
Publicado en: PRE, 2022, ISSN 2470-0045
Editor: APS

A deep learning approach to the structural analysis of proteins

Autores: Marco Giulini, Raffaello Potestio
Publicado en: Interface Focus, Edición 9/3, 2019, Página(s) 20190003, ISSN 2042-8898
Editor: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0003

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

Autores: Patrick Diggins, Changjiang Liu, Markus Deserno, Raffaello Potestio
Publicado en: Journal of Chemical Theory and Computation, Edición 15/1, 2018, Página(s) 648-664, ISSN 1549-9618
Editor: 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

Autores: Thomas Tarenzi, Vania Calandrini, Raffaello Potestio, Paolo Carloni
Publicado en: Journal of Chemical Theory and Computation, Edición 15/3, 2019, Página(s) 2101-2109, ISSN 1549-9618
Editor: American Chemical Society
DOI: 10.1021/acs.jctc.9b00040

Envisioning data sharing for the biocomputing community

Autores: Enrico Riccardi, Sergio Pantano, Raffaello Potestio
Publicado en: Interface Focus, Edición 9/3, 2019, Página(s) 20190005, ISSN 2042-8898
Editor: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0005

Multi-resolution simulations of intracellular processes

Autores: Radek Erban, Sarah Harris, Raffaello Potestio
Publicado en: Interface Focus, Edición 9/3, 2019, Página(s) 20190028, ISSN 2042-8898
Editor: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0028

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

Autores: Maziar Heidari, Kurt Kremer, Ramin Golestanian, Raffaello Potestio, Robinson Cortes-Huerto
Publicado en: The Journal of Chemical Physics, Edición 152/19, 2020, Página(s) 194104, ISSN 0021-9606
Editor: American Institute of Physics
DOI: 10.1063/1.5143268

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

Autores: Raffaele Fiorentini, Kurt Kremer, Raffaello Potestio
Publicado en: Proteins: Structure, Function, and Bioinformatics, 2020, ISSN 0887-3585
Editor: Wiley-Liss Inc
DOI: 10.1002/prot.25954

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

Autores: Thomas Tarenzi, Gianluca Lattanzi, Raffaello Potestio
Publicado en: Biochimica et Biophysica Acta (BBA) - Biomembranes, 2022, ISSN 0005-2736
Editor: Elsevier BV
DOI: 10.1016/j.bbamem.2022.183970

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

Autores: Thomas Tarenzi; Marta Rigoli; Raffaello Potestio
Publicado en: Scientific Reports, Vol 11, Iss 1, Pp 1-12 (2021), Edición 1, 2021, ISSN 2045-2322
Editor: 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

Autores: Thomas Tarenzi, Marta Rigoli, Giovanni Mattiotti, Raffaello Potestio
Publicado en: Applied Sciences, 2022, ISSN 2076-3417
Editor: MDPI
DOI: 10.3390/app12147157