Katrin Schöning-Stierand (UHH), Christiane Ehrt (UHH) (BioData)
18.11.2021 (5 PM - 7 PM)
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 the thus published 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 with these tools 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.
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
General knowledge of proteins and their role in life sciences
AlphaFold, protein structures, binding site prediction, binding site comparison, molecular docking, molecular modeling, ProteinsPlus
Tools: ProteinsPlus-Tools DoGSite, SIENA, GeoMine and JAMDA