Katrin Schöning-Stierand, Christine Ehrt, Matthias Rarey (BioData)
Online - GCB 2021
Three-dimensional protein structures are a fundamental basis for understanding, modulating, and manipulating protein functionality. With almost 175,000 structures (access date: March 1st, 2021), the Protein Data Bank (PDB) is one of the most important bioinformatics resources for life sciences. Roughly 1,000 structures are SARS-CoV-2 structures, forming a good basis for structure-based modeling processes.
In this workshop, we present the ProteinsPlus server enriching structural knowledge from the PDB by additional computed information required for typical biological research questions. ProteinsPlus enables easy access to this information for all researchers in the fields of molecular life sciences. The provided computational services comprise various tools for the assessment, representation, preprocessing, and interconnection of structural data. Many of the provided tools focus on protein binding pockets and molecular interactions to small molecules due to their relevance for drug design.
Participants will get to know a combination of tools and web services for searching and analyzing protein structure data. The focus will be on protein preparation for molecular docking scenarios related to COVID-19. We will work with the ProteinsPlus web service that contains a diverse range of software solutions for the analysis of protein structures and its application in molecular modeling approaches.
This course is designed for life and computer scientists with interest in protein structures, but only very basic experience in 3D modeling. Topics include: Finding and selecting protein structure data, evaluating the quality of experimental data, preprocessing structure data for modeling, first modeling steps like the analysis of binding site properties and conformational flexibility, fully automated docking. The usage of the ProteinsPlus tools is free and open to all users.
General knowledge of proteins and their role in life sciences
Protein structures, protein-ligand interactions, molecular modeling, structure-to-function relationships, cheminformatics, ProteinsPlus, BRENDA, EnzymeStructures, KNIME