Exploring AlphaFold Structures with the ProteinsPlus Web Server

Katrin Schöning-Stierand

Interested in working with AlphaFold structures? Start exploring them supported by ProteinsPlus tools!

Contents: Artificial intelligence-based protein structure predictions with AlphaFold enable unprecedented access to high-quality models of proteins with yet unknown folds. These structures are now readily accessible using the AlphaFold Protein Structure Database (https://alphafold.ebi.ac.uk/). However, these structures miss important annotations and need to be carefully processed for further molecular modeling or even structure-based drug design studies. To enable on-the-fly structural modeling for these structures, we integrated these structures in our ProteinsPlus web server (https://proteins.plus). The web server offers tools for binding site prediction (DoGSite), binding site comparison (SIENA and GeoMine) and molecular docking (JAMDA) for the annotation and investigation of the AlphaFold structures. Besides the detection of potential binding sites on the protein’s surface, an in-depth exploration is possible through an easy-to-use user interface. Through a short introduction of the web server tools and a comprehensive demo session on exploring AlphaFold structures the participants will gain knowledge on applying these tools to their own predicted structure of interest. After these introductory sessions, the attendees will be able to explore a target of interest on the ProteinsPlus web server, ask questions and get support by the educators. 

Learning goals: This course is designed for life and computer scientists with interest in protein structures and structure-based drug design, but only very basic experience. Topics include: Finding binding sites in protein structure models generated with AlphaFold, detecting related binding sites and molecular docking of known ligands.
Usage of ProteinsPlus, with focus on DoGSite, SIENA, GeoMine and JAMDA

Prerequisites: General knowledge of proteins and their role in life sciences

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Exploring AlphaFold Structures with the ProteinsPlus Web Server

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Exploring AlphaFold Structures with the ProteinsPlus Web Server

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