Title :

Surface-based protein domains retrieval methods from a SHREC2021 challenge

Author(s) :

Langenfeld, Florent [Auteur]
Laboratoire Génomique, bioinformatique et chimie moléculaire [GBCM]
Aderinwale, Tunde [Auteur]
Department of Computer Science [Purdue]
Christoffer, Charles [Auteur]
Department of Computer Science [Purdue]
Shin, Woong-Hee [Auteur]
Terashi, Genki [Auteur]
Purdue University [West Lafayette]
Wang, Xiao [Auteur]
Department of Computer Science [Purdue]
Kihara, Daisuke [Auteur]
Purdue University [West Lafayette]
Department of Computer Science [Purdue]
Benhabiles, Halim [Auteur]
JUNIA [JUNIA]
Bio-Micro-Electro-Mechanical Systems - IEMN [BIOMEMS - IEMN]
Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 [IEMN]
Hammoudi, Karim [Auteur]
Université de Strasbourg [UNISTRA]
Institut de Recherche en Informatique Mathématiques Automatique Signal - IRIMAS - UR 7499 [IRIMAS]
Cabani, Adnane [Auteur]
École Supérieure d’Ingénieurs en Génie Électrique [ESIGELEC]
Windal, Feryal [Auteur]
JUNIA [JUNIA]
Bio-Micro-Electro-Mechanical Systems - IEMN [BIOMEMS - IEMN]
Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 [IEMN]
Melkemi, Mahmoud [Auteur]
Université de Strasbourg [UNISTRA]
Institut de Recherche en Informatique Mathématiques Automatique Signal - IRIMAS - UR 7499 [IRIMAS]
Otu, Ekpo [Auteur]
Aberystwyth University
Zwiggelaar, Reyer [Auteur]
Aberystwyth University
Hunter, David [Auteur]
Aberystwyth University
Liu, Yonghuai [Auteur]
Edge Hill University
Sirugue, Léa [Auteur]
Laboratoire Génomique, bioinformatique et chimie moléculaire [GBCM]
Nguyen, Huu-Nghia [Auteur]
Vietnam National University - Ho Chi Minh City [VNU-HCM]
Nguyen, Tuan-Duy [Auteur]
Vietnam National University - Ho Chi Minh City [VNU-HCM]
Nguyen-Truong, Vinh-Thuyen [Auteur]
Vietnam National University - Ho Chi Minh City [VNU-HCM]
Le, Danh [Auteur]
Vietnam National University - Ho Chi Minh City [VNU-HCM]
Nguyen, Hai-Dang [Auteur]
Vietnam National University - Ho Chi Minh City [VNU-HCM]
Tran, Minh-Triet [Auteur]
Vietnam National University - Ho Chi Minh City [VNU-HCM]
Montès, Matthieu [Auteur]
Laboratoire Génomique, bioinformatique et chimie moléculaire [GBCM]

Journal title :

Journal of Molecular Graphics and Modelling

Pages :

108103

Publisher :

Elsevier

Publication date :

2022-03

ISSN :

1093-3263

English keyword(s) :

2000 MSC: 92-08
Proteins surface
SHREC2021

HAL domain(s) :

Sciences de l'ingénieur [physics]

English abstract : [en]

Proteins are essential to nearly all cellular mechanism and the effectors of the cells activities. As such, they often interact through their surface with other proteins or other cellular ligands such as ions or organic ...
Show more >Proteins are essential to nearly all cellular mechanism and the effectors of the cells activities. As such, they often interact through their surface with other proteins or other cellular ligands such as ions or organic molecules. The evolution generates plenty of different proteins, with unique abilities, but also proteins with related functions hence similar 3D surface properties (shape, physico-chemical properties, …). The protein surfaces are therefore of primary importance for their activity. In the present work, we assess the ability of different methods to detect such similarities based on the geometry of the protein surfaces (described as 3D meshes), using either their shape only, or their shape and the electrostatic potential (a biologically relevant property of proteins surface). Five different groups participated in this contest using the shape-only dataset, and one group extended its pre-existing method to handle the electrostatic potential. Our comparative study reveals both the ability of the methods to detect related proteins and their difficulties to distinguish between highly related proteins. Our study allows also to analyze the putative influence of electrostatic information in addition to the one of protein shapes alone. Finally, the discussion permits to expose the results with respect to ones obtained in the previous contests for the extended method. The source codes of each presented method have been made available online.Show less >

Language :

Anglais

Peer reviewed article :

Oui

Audience :

Internationale

Popular science :

Non

Comment :

publication dans une revue suite à la communication hal-03467479 (SHREC 2021: surface-based protein domains retrieval)

Collections :

• Institut d'Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR 8520

Source :

Harvested from HAL