2D zernike polynomial expansion: finding the protein-protein binding regions
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- dc.contributor.author Milanetti, Edoardo
- dc.contributor.author Miotto, Mattia
- dc.contributor.author Di Rienzo, Lorenzo
- dc.contributor.author Monti, Michele
- dc.contributor.author Gosti, Giorgio
- dc.contributor.author Ruocco, Giancarlo
- dc.date.accessioned 2022-04-27T10:57:47Z
- dc.date.available 2022-04-27T10:57:47Z
- dc.date.issued 2020
- dc.description.abstract We present a method for efficiently and effectively assessing whether and where two proteins can interact with each other to form a complex. This is still largely an open problem, even for those relatively few cases where the 3D structure of both proteins is known. In fact, even if much of the information about the interaction is encoded in the chemical and geometric features of the structures, the set of possible contact patches and of their relative orientations are too large to be computationally affordable in a reasonable time, thus preventing the compilation of reliable interactome. Our method is able to rapidly and quantitatively measure the geometrical shape complementarity between interacting proteins, comparing their molecular iso-electron density surfaces expanding the surface patches in term of 2D Zernike polynomials. We first test the method against the real binding region of a large dataset of known protein complexes, reaching a success rate of 0.72. We then apply the method for the blind recognition of binding sites, identifying the real region of interaction in about 60% of the analyzed cases. Finally, we investigate how the efficiency in finding the right binding region depends on the surface roughness as a function of the expansion order.
- dc.description.sponsorship Michele Monti acknowledges funding through the H2020 project IN-FORE 825080
- dc.format.mimetype application/pdf
- dc.identifier.citation Milanetti E, Miotto M, Di Rienzo L, Monti M, Gosti G, Ruocco G. 2D zernike polynomial expansion: finding the protein-protein binding regions. Comput Struct Biotechnol J. 2020 Dec 4;19:29-36. DOI:10.1016/j.csbj.2020.11.051
- dc.identifier.doi http://dx.doi.org/10.1016/j.csbj.2020.11.051
- dc.identifier.issn 2001-0370
- dc.identifier.uri http://hdl.handle.net/10230/52911
- dc.language.iso eng
- dc.publisher Elsevier
- dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/825080
- dc.rights © 2020 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.subject.other Proteïnes
- dc.subject.other Molècules
- dc.title 2D zernike polynomial expansion: finding the protein-protein binding regions
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion