German Conference on Bioinformatics (GCB) 2020

14 - 17 September 2020,
Virtual Conference
 

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WS6: Protein Structure Fundamentals: Searching - Analyzing – Modeling

Instructors:

Katrin Schöning-Stierand and Matthias Rarey
Universität Hamburg, ZBH – Center for Bioinformatics, Hamburg, Germany

Abstract

Three-dimensional protein structures are a fundamental basis for understanding, modulating, and manipulating protein functionality. With over 155,000 structures, the Protein Data Bank (PDB) is one of the most important bioinformatics resources for life science.
In this workshop, we present the ProteinsPlus server [1] enriching structural knowledge from the PDB by additional computed information required for common 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 various research questions.
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 function and related interactions to small molecules. 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.
[1] https://proteins.plus : R. Fährrolfes, S. Bietz, F. Flachsenberg, A. Meyder, E. Nittinger, T. Otto, A. Volkamer, M. Rarey, Nucleic Acids Res. 2017, 45 (W1), W337–W343.

Learning goals:

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. Usage of ProteinsPlus is free and open to all users.

Prerequisites:

General knowledge of proteins and their role in life sciences.

Keywords:

Protein structures, protein-ligand interactions, molecular modeling, structure-to-function relationships, ProteinsPlus, EnzymeStructures

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