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Introduction to structural bioinformatics for evolutionary analysis

Date:

Thursday, 3rd September

Time:

17:00 to 20:00 (CEST)

Instructors and helpers 

  • 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

Summary

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.

Target audience

This is a hands-on tutorial intended for a beginner level audience. This tutorial is aimed at graduate students and post-doctoral researchers who are applying or planning to apply bioinformatics methods to analyse protein structural data in their research.
No previous experience in structural bioinformatics is required.

Maximum participants

Unlimited.

Requirements

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

Schedule

Time (CEST)
Details
17:00 - 17:40 Introduction to web tools for protein structure classification
17:40 - 18:20 Searching for homologous protein structures
18:20 – 18:50 Overview of pairwise structure superimposition tools
18:50 – 19:20 Correspondences between protein sequence and structure
19:20 – 19.50 Conservation and covariation
19:20 – 19.50 Wrap-up and feedback