AlloViz: A tool for the calculation and visualisation of protein allosteric communication networks

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  • dc.contributor.author Nerín-Fonz, Francho
  • dc.contributor.author Caprai, Camilla
  • dc.contributor.author Morales Pastor, Adrián
  • dc.contributor.author Lopez-Balastegui, Marta
  • dc.contributor.author Aranda García, David
  • dc.contributor.author Giorgino, Toni
  • dc.contributor.author Selent, Jana
  • dc.date.accessioned 2025-04-16T06:38:22Z
  • dc.date.available 2025-04-16T06:38:22Z
  • dc.date.issued 2024
  • dc.description.abstract Allostery, the presence of functional interactions between distant parts of proteins, is a critical concept in the field of biochemistry and molecular biology, particularly in the context of protein function and regulation. Understanding the principles of allosteric regulation is essential for advancing our knowledge of biology and developing new therapeutic strategies. This paper presents AlloViz, an open-source Python package designed to quantitatively determine, analyse, and visually represent allosteric communication networks on the basis of molecular dynamics (MD) simulation data. The software integrates well-known techniques for understanding allosteric properties simplifying the process of accessing, rationalising, and representing protein allostery and communication routes. It overcomes the inefficiency of having multiple methods with heterogeneous implementations and showcases the advantages of using MD simulations and multiple replicas to obtain statistically sound information on protein dynamics; it also enables the calculation of "consensus-like" scores aggregating methods that consider multiple structural aspects of allosteric networks. We demonstrate the features of AlloViz on two proteins: β-arrestin 1, a key player for regulating G protein-coupled receptor (GPCR) signalling, and the protein tyrosine phosphatase 1B, an important pharmaceutical target for allosteric inhibitors. The software includes comprehensive documentation and examples, tutorials, and a user-friendly graphical interface.
  • dc.description.sponsorship DAG acknowledges financial support from the Catalan Department of Business and Innovation [2020FISDU/487]. TG acknowledges funding from the Spoke 7 of the National Centre for HPC, Big Data and Quantum Computing [CN00000013, CUP B93C22000620006] and from PRIN 2022 [BioCat4BioPol, CUP B53D23015140006] from the Ministero dell'Università e Ricerca, funded by the European Union – NextGenerationEU. JS acknowledges funding from MICIU/AEI/10.13039/501100011033 and the ERDF/EU (grant number PID2022-137161OB-I00). JS acknowledges further funding from the Horizon Europe Project OBELISK under the grant agreement 101080465. JS has been financially supported by the Instituto de Salud Carlos III FEDER [PI18/00094] and the ERA-NET NEURON & Ministry of Economy, Industry, and Competitiveness [AC18/00030]. Funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Health and Digital Executive Agency (HADEA). Neither the European Union nor the granting authority can be held responsible for them. We acknowledge the CINECA awards under the ISCRA initiative for the availability of high performance computing resources and support. FNF, AMP, MLB, DAG, TG and JS have been members of COST Action CA18133 “ERNEST”.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Nerín-Fonz F, Caprai C, Morales-Pastor A, Lopez-Balastegui M, Aranda-García D, Giorgino T, et al. AlloViz: A tool for the calculation and visualisation of protein allosteric communication networks. Comput Struct Biotechnol J. 2024 Apr 25;23:1938-44. DOI: 10.1016/j.csbj.2024.04.047
  • dc.identifier.doi http://dx.doi.org/10.1016/j.csbj.2024.04.047
  • dc.identifier.issn 2001-0370
  • dc.identifier.uri http://hdl.handle.net/10230/70146
  • dc.language.iso eng
  • dc.publisher Elsevier
  • dc.relation.ispartof Comput Struct Biotechnol J. 2024 Apr 25;23:1938-44
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/HE/101080465
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PE/PID2022-137161OB-I00
  • dc.rights © 2024 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/4.0/
  • dc.title AlloViz: A tool for the calculation and visualisation of protein allosteric communication networks
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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