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VAriable ResolutIon Algorithms for macroMOLecular Simulation

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Publications

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, 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, 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, 16/11, 2020, Page(s) 6795-6813, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.0c00676

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), 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), 1, 2021, ISSN 2296-889X
Publisher: Frontiers Media S.A.
DOI: 10.3389/fmolb.2021.637396

A deep learning approach to the structural analysis of proteins

Author(s): Marco Giulini, Raffaello Potestio
Published in: Interface Focus, 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, 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, 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, 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, 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, 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), 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

An information theory-based approach for optimal model reduction of biomolecules

Author(s): Giulini, Marco; Menichetti, Roberto; Shell, M. Scott; Potestio, Raffaello
Published in: 1, 2020
Publisher: Cornell University

Accelerating the identification of informative reduced representations of proteins with deep learning for graphs

Author(s): Errica, Federico; Giulini, Marco; Bacciu, Davide; Menichetti, Roberto; Micheli, Alessio; Potestio, Raffaello
Published in: 1, 2020
Publisher: Cornell Univ.