Bioinformatics Tools for Protein Structure, Disorder and Interaction Analysis

Course description

Cellular signaling is carried out by dynamic multi-molecular complexes that may coalesce, split apart, relocate, gain and lose individual regulatory proteins. The state of these complexes can be switched by post translational modifications, and once the signal has been transmitted and complexes are no longer needed, they can be fully dismantled. Despite their central importance, for the most part these regulatory complexes are poorly understood. A protein’s modular architecture determines the types of interactions it can establish. Many of these interactions are mediated by flexible or “natively unstructured” regions that code important functions through modular elements termed “linear motifs”. This Workshop will present a variety of bioinformatics tools that can be used to explore a protein’s functional architecture as a tool towards predicting and testing its possible functions and interactions.

SCHEDULE:

Tuesday, November 21^st

9:00-9:30 am: Registration

9:15 am-12:30 pm. Course Intro (Aula 1).

9:30-10:15 am: Welcome. Presentation of teachers and students.

10:15-11:00 am: Course Introduction I (Lucia Chemes).

Coffee Break 11:00-11:30 am

11:30-12:30: Lecture by Toby Gibson. Title: warm up and experimental tips.

12:30-1:30 pm: Lunch on own

1:30-3:00 pm: Practical Session 1: Protein databases and related annotation resources (UNIPROT, Pfam).

Coffee Break 3-3:30 pm

3:30-5 pm: Practical Session 2: Tools and resources for the analysis of the structural architecture of a protein (PDB, InterPro, TMHMM).

Wednesday, November 22^nd

9:00-11:00 am: Practical Session 3: Analysis and prediction of intrinsically disordered regions (JPred, IUPRED, Anchor, Disprot, MobiDB).

Coffee break at IIB-INTECH 11-11:30pm

11:30hs-12:30hs: Lecture by Toby Gibson. Title: Complexity of PPIs. (IIB-UNSAM)

12:30-1:30 pm: Lunch on own

1:30 - 3:30 pm: Practical Session 4: Understanding linear motifs & intrinsically disordered regions (ELM, SLiMSearch, ProViz).

Coffee Break 3:30-4pm

4:00-6:00 pm: Practical Session 5: Revealing interactive features in protein multiple sequence alignments with Jalview.

Thursday, November 23^rd

9:00-10:45 am: Talks:

Gonzalo de Prat Gay. Talk title: Experimental investigation of IDPs.

Ignacio Sánchez. Talk title: Bioinformatics approaches to the study of IDPs.

Coffee break 10:45-11:15 am

11:15-1:15 pm: Practical Session 6: Visualizing protein structures and interaction interfaces with UCSF Chimera.

1:15-2:00 pm: Lunch on own

2:00-3:15 pm: Practical Session 7: Protein association networks with STRING. Protein networks (Reactome/KEGG).

Coffee Break 3:15-3:45 pm

3:45-5:00 pm: Practical Session 8: Practical with you own protein and QA session.

5:00-5:30 pm: Discussion and feedback.

Total duration: 24 hours.