{"id":9411,"date":"2024-05-12T17:43:22","date_gmt":"2024-05-12T16:43:22","guid":{"rendered":"https:\/\/www.afmb.univ-mrs.fr\/?post_type=event&p=9411"},"modified":"2024-05-12T18:44:50","modified_gmt":"2024-05-12T17:44:50","slug":"n-terrapons-team-guest-tatiana-galochkina-laboratoire-biologie-integree-du-globule-rouge-inserm-u-paris-cite-ia-et-interactions-proteines-glucides","status":"publish","type":"event","link":"https:\/\/www.afmb.univ-mrs.fr\/en\/event\/n-terrapons-team-guest-tatiana-galochkina-laboratoire-biologie-integree-du-globule-rouge-inserm-u-paris-cite-ia-et-interactions-proteines-glucides\/","title":{"rendered":"N. Terrapon’s team guest: Tatiana Galochkina, laboratoire Biologie Int\u00e9gr\u00e9e du Globule Rouge, Inserm \/ U. Paris Cit\u00e9 \u2013 \u201cAnalysis and prediction of carbohydrate binding sites on protein surface\u201d"},"content":{"rendered":"\n

Abstract<\/strong><\/p>\n\n\n\n

Protein-carbohydrate (PC) interactions govern a wide variety of biological processes and play a crucial role in the development of different diseases. During the last decades, the release of an impressive amount of data on carbohydrate-binding proteins led to the emergence of first data driven methods for prediction of carbohydrate binding sites. Nevertheless, the performance of such models remains limited as compared to similar bioinformatics problems, and its correct evaluation is hindered by the lack of the reliable and non-redundant datasets. In the current study, we address this challenge and perform an exhaustive analysis of the diversity of PC interfaces and of its impact on prediction models accuracy.\u00a0<\/p>\n\n\n\n

We have gathered and annotated all the available information on PC interfaces found in the Protein Data Bank (PDB) in a user-friendly web-server, DIONYSUS : https:\/\/www.dsimb.inserm.fr\/DIONYSUS\/<\/a>. Using a customized algorithm, we identified >46k PC complexes interacting with one of 3k carbohydrate-containing ligands of the PDB (increasing the number of these structures by orders of magnitude as compared to 900 ligand names available in the Chemical Component Dictionary). We performed an exhaustive study of PC interface diversity at different levels: by functional class of interaction, protein sequence identity and local geometrical similarity between the interfaces. Furthermore, we identified representative structures of different classes of PC interactions and used them to annotate PC complexes with missing functional information. <\/p>\n\n\n\n

Finally, the developed database allows us to train several deep learning models based on protein language model encoding of the protein sequence combined to molecular graphs to encode protein structure. In-depth analysis of our model performance and its comparison to the previously published methods demonstrates significant improvements of carbohydrate binding site identification as well as highlights the remaining challenges in the field.<\/p>\n\n\n\n

Tatiana Galochkina est MCF \u00e0 Universit\u00e9 Paris Cit\u00e9, Facult\u00e9 de Sciences, UFR Sciences du Vivant depuis 2019 et fait partie de l\u2019\u00c9quipe DSIMB du laboratoire BIGR (Biologie int\u00e9gr\u00e9e du globule rouge, INSERM UMRS 1134 et Universit\u00e9 Paris Cit\u00e9). Ses principaux int\u00e9r\u00eats de recherche incluent la mod\u00e9lisation de syst\u00e8mes mol\u00e9culaires complexes et le d\u00e9veloppement de mod\u00e8les pr\u00e9dictifs pour la dynamique et les interactions des prot\u00e9ines. Elle a obtenu un projet ANR jeune chercheur intitul\u00e9 \u201cSugarPred : Deciphering protein-carbohydrate interactions\u201c. En effet, les interactions prot\u00e9ines-glucides jouent un r\u00f4le crucial dans divers processus biologiques. Cependant, ces interactions restent peu \u00e9tudi\u00e9es en raison de la difficult\u00e9 de leur description exp\u00e9rimentale. L\u2019objectif principal de son projet est la classification pr\u00e9cise et le d\u00e9veloppement d\u2019outils bas\u00e9s sur l\u2019apprentissage automatique pour pr\u00e9dire les sites potentiels de liaison des glucides \u00e0 la surface des prot\u00e9ines. Plus d\u2019informations sur https:\/\/sites.google.com\/view\/tatiana-galochkina<\/a><\/em><\/p>\n","protected":false},"template":"","events_category":[15],"class_list":["post-9411","event","type-event","status-publish","hentry","events_category-seminar","entry"],"_links":{"self":[{"href":"https:\/\/www.afmb.univ-mrs.fr\/en\/wp-json\/wp\/v2\/event\/9411","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.afmb.univ-mrs.fr\/en\/wp-json\/wp\/v2\/event"}],"about":[{"href":"https:\/\/www.afmb.univ-mrs.fr\/en\/wp-json\/wp\/v2\/types\/event"}],"wp:attachment":[{"href":"https:\/\/www.afmb.univ-mrs.fr\/en\/wp-json\/wp\/v2\/media?parent=9411"}],"wp:term":[{"taxonomy":"events_category","embeddable":true,"href":"https:\/\/www.afmb.univ-mrs.fr\/en\/wp-json\/wp\/v2\/events_category?post=9411"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}