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SHREC 2021: Surface-based Protein Domains Retrieval

Florent Langenfeld, Tunde Aderinwale, Charles Christoffer, Woong-Hee Shin, Genki Terashi, Xiao Wang, Daisuke Kihara, Halim Benhabiles, Karim Hammoudi, Adnane Cabani, Feryal Windal, Mahmoud Melkemi (+12 others)
2021 Eurographics Workshop on 3D Object Retrieval, EG 3DOR  
In the present work, we assess the ability of five methods to retrieve similar protein surfaces, using either their shape only (3D meshes), or their shape and the electrostatic potential at their surface  ...  Proteins are essential to nearly all cellular mechanism, and often interact through their surface with other cell molecules, such as proteins and ligands.  ...  Acknowledgments The authors thank the 3DOR 2021 Workshop organizing committee for maintaining this workshop despite the current COVID-19 pandemic. F. Langenfeld, L. Sirugue and M.  ... 
doi:10.2312/3dor.20211308 fatcat:77a6vuyr5jdkzpehp35ojy4ccq

SHREC 2021: Classification in Cryo-electron Tomograms

Ilja Gubins, Marten L. Chaillet, Gijs Van Der Schot, M. Cristina Trueba, Remco C. Veltkamp, Friedrich Förster, Xiao Wang, Daisuke Kihara, Emmanuel Moebel, Nguyen P. Nguyen, Tommi White, Filiz Bunyak (+11 others)
2021 Eurographics Workshop on 3D Object Retrieval, EG 3DOR  
In this paper, we have evaluated seven different methods of finding and classifying proteins.  ...  We show that learning-based approaches can achieve notably better localization and classification performance than TM.  ... © 2021 The Author(s) Eurographics Proceedings © 2021 The Eurographics Association.  ... 
doi:10.2312/3dor.20211307 fatcat:4ogenb2jmzhq3pi52fjf2sknzq

SHREC 2021 track: Retrieval and classification of protein surfaces equipped with physical and chemical properties [article]

Andrea Raffo, Ulderico Fugacci, Silvia Biasotti, Walter Rocchia, Yonghuai Liu, Ekpo Otu, Reyer Zwiggelaar, David Hunter, Evangelia I. Zacharaki, Eleftheria Psatha, Dimitrios Laskos, Gerasimos Arvanitis (+12 others)
2021 arXiv   pre-print
This paper presents the methods that have participated in the SHREC 2021 contest on retrieval and classification of protein surfaces on the basis of their geometry and physicochemical properties.  ...  Retrieval and classification performances, with respect to the single protein or the existence of common sub-sequences, are analysed according to a number of information retrieval indicators.  ...  This project is co-funded by the project "TEACUP: Metodi e TEcniche innovative per lo sviluppo di librerie per la modellazione, l'Analisi e il confronto CompUtazionale di Proteine", POR FSE, Programma  ... 
arXiv:2105.05221v1 fatcat:ooj7logkevbxbpljqwjszjex54

Comparative Evaluation of Shape Retrieval Methods on Macromolecular Surfaces: An Application of Computer Vision Methods in Structural Bioinformatics

Mickael Machat, Florent Langenfeld, Daniela Craciun, Léa Sirugue, Taoufik Labib, Nathalie Lagarde, Maxime Maria, Matthieu Montes, Alfonso Valencia
2021 Bioinformatics  
paradigm towards a protein structure-surface(s)-function paradigm.  ...  This work illustrates the interest for the protein surface shape as a higher-level representation of the protein structure that 1) abstracts the underlying protein sequence, structure or fold, 2) allows  ...  guest on 12 July 2021 Table 4 .  ... 
doi:10.1093/bioinformatics/btab511 pmid:34247232 pmcid:PMC8652110 fatcat:zry564cz3rfwvnsmcuowi5cow4

Dense Graph Convolutional Neural Networks on 3D Meshes for 3D Object Segmentation and Classification [article]

Wenming Tang Guoping Qiu
2021 arXiv   pre-print
Based on this new graph representation, we then design a densely connected graph convolutional block which aggregates local and regional features as the key construction component to build effective and  ...  Paraboschi, Shape retrieval contest 2007: Water- tight models track, SHREC competition 8 (7). 32  ...  and retrieval tasks by combining CNN and GCN.  ... 
arXiv:2106.15778v1 fatcat:bja4cmbuxvd33p6aogftfpwqeq

Similarity reasoning for local surface analysis and recognition

We go beyond the retrieval of models or surface patches in a collection of models, facing the recognition of geometric patterns across digital models with different overall shape.  ...  Finally, the recognition of patterns adds a further perspective in the exploration of (large) 3D data collections, especially in the cultural heritage domain.  ...  3D retrieval) and in generic or domain specific models (CAD, biometrics, architectural, protein, etc.).  ... 
doi:10.15167/moscoso-thompson-elia_phd2021-03-29 fatcat:5o33whvppre6zbazjikovssvnm