• Claudia Alvarez Carreño | Georgia Institute of Technology, United States
• Alma Carolina Sanchez Rocha | Charles University, Prague, Czech Republic
• Vyacheslav Tretyachenko | Charles University, Prague, Czech Republic

Three-dimensional structure analyses can provide a biophysical understanding of how proteins work and evolve. Most evolutionary studies are based solely on sequence data. However, point mutations and sequence rearrangements have implications for protein structure. This tutorial will familiarize participants with straightforward bioinformatics protocols for combining evolutionary information and biophysical understanding of proteins. Furthermore, many proteins contain unstructured regions in their native state. We will provide cutting edge bioinformatics algorithms to analyze both folded protein domains and intrinsically disordered proteins and regions. We will focus on protein structure classification, structure comparison methods and evolutionary analyses.

This workshop is intended for a beginner level audience. No previous experience in structural bioinformatics is required. During the first part of the workshop, participants will learn how to access structural data resources and how to select, retrieve and manipulate quality information. Next, we will introduce algorithms to evaluate the roles of specific residues in function and fold conservation. In the last part of the workshop, we will focus on tools for integrating structure information and evolutionary models.

Learning outcomes

By the end of the workshop, attendants should be able to:

• Search for structures in the Protein Data Bank and protein structure classification databases.
• Know how to use web-based and command line algorithms for structure superimposition.
• Calculate widely used scores to evaluate structure superimposition.
• Identify conserved motifs in sequence and in structure.
• Predict intrinsically disordered regions in amino acid sequences.
• Use structure superimposition to guide phylogenetic analysis.

All participants are required to have access to a laptop/personal computer with a text editor installed.