EMBL-EBI Workshop: Bioinformatics tools for exploring protein biology, Iasi, Romania

Date:

 Thursday 4 Friday 5 April 2019

Venue: 

Alexandru Ioan Cuza University - Bulevardul Carol I nr. 11, 700506,  Iasi, Romania

Application opens: 

Thursday 10 January 2019

Application deadline: 

Sunday 10 March 2019

Participation: 

Open application with selection

Contact: 

Marina Pujol

Registration fee: 

Registration closed

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Course Overview

This two-day workshop will introduce participants to bioinformatics approaches for analysis biological data from resources such as UniProt and the PDBe. Day 1 will cover introductory programming in UNIX and python, sequence similarity searching, and how to navigate and use the protein sequence database UniProt. Day 2 will cover methods to access and retrieve data programmatically, the macromolecular structure database Protein Data Bank in Europe, and end with a talk and panel discussion on artificial intelligence’s role in protein structure prediction.

Activities will include interactive presentations and practical exercises delivered by experienced trainers, which will give trainees hands-on experience.
 

Audience

This workshop is aimed at postgraduates (Masters and PhD students) as well as young researchers working with protein sequences and structures.

An undergraduate level understanding of molecular biology and protein structures is necessary. No prior experience of bioinformatics is required.
 

Modules

  • introduction-embl-ebi-resources-and-tools
  • protein-sequence-databases
  • introduction-macromolecular-structure-pdbe

Learning outcomes

After this course you should be able to: 

  • Identify information about all aspects of a protein such as function, interactions and disease association
  • Investigate protein homology via sequence similarity searches and alignments
  • Use UniProt to connect to specialized resources in different areas of biology
  • Search, retrieve and assess the quality of structural data from the PDB archive
  • Visualise and analyse structures, including viewing annotations
  • View protein-ligand interactions and identify structurally similar proteins

Programme

Day 1 – Thursday 4 April 2019
09:00-09:30 Welcome note and coffee Organizers
09:30-11:00 Introduction to programming: Useful commands in Unix shell and Python Claudiu Mihăilă
11:00-11:30 Coffee Break
11:30-12:30 Introduction to sequence searching and alignments. DNA/RNA vs proteins sequences. Protein sequence and Function Anna Marobotti
12:30-13:30 Lunch
13:30-13:45 Introduction to EMBL-EBI resources and tools Hema Bye-A-Jee
13:45-15:30 Protein Sequence Databases: UniProt Hema Bye-A-Jee
15:30-16:00 Coffee Break
16:00-17:00 Protein Sequence Databases: UniProt Hema Bye-A-Jee
17:00 Talk Anna Marabotti
19:00 Festive dinner
Day 2 – Friday 5 April 2019
09:00-10:00 Introduction to programming. Programmatic access to public databases and data retrieval Claudiu Mihăilă
10:00-10:30 Coffee Break
10:30-12:30 Introduction to macromolecular structure at the PDBe Matt Conroy
12:30-13:30 Lunch
13:30-15:30 Introduction to macromolecular structure at the PDBe Matt Conroy
15:30-16:00 Coffee Break
16:00-16:30 Talk: Modeling biomolecular structures in the twilight zone and beyond Andrei-Jose Petrescu
16:30-17:00 Panel Discussion: AI’s contribution to construct predictions of protein structures All speakers and trainers
17:00 Farewell  
18:30 Beer and science event  

Additional information:

For more information, please see the course webpage on RSBI.ro here.