Location to be confirmed VUB U-residence Date: after the summer 2019
Instructor: Niloofar Shirvanizadeh
There are now well over 130 million protein sequences available from Uniprot, and for only a small fraction of these (about 2%) structural information is available from the Protein Data Bank. Uniprot provides a mix of manual and automatic functional and structural annotations for these sequences, but when working on a particular research question you might want to obtain more detailed insights into the possible behavior of the protein(s) you are interested in.
In this workshop, we address how to predict features of proteins from their sequence only, using Python scripts to access APIs of web services available online. We will introduce single-sequence based predictions of biophysical characteristics of proteins (e.g. DynaMine for backbone dynamics), methods that use multiple sequence alignments (e.g. I-TASSER), and methods that determine the difference between a protein and its mutant form (e.g. DEOGEN2). We will also show how the results of these predictions can be combined and analysed using a protein case study.
| Time | Activity |
|---|---|
| 9:30-10:15 | Introduction |
| 10:15-11:00 | Python set up |
| 11:00-11:15 | Coffee Break |
| 11:15-12:30 | Bio2byte services (DynaMine, DisoMine, DEOGEN2, EFoldMine) |
| 12:30-13:30 | Lunch |
| 13:30-14:45 | Other bioinformatics services (Jpred 3, ELM, I-TASSER, PROFEAT, TMHMM, STRING, SiteMap) |
| 14:45-15:00 | Coffee Break |
| 15:00-17:00 | Case Study |