Educators:
Toby Gibson, Malvika Sharan, Marc Gouw, Manjeet Kumar, Michael Kühn (HD-HuB)

Date:
26/02/2018 - 28/02/2018
09:30 - 17:00

Location:
ATC Computer Training Lab

Contents:
This course will introduce online and open-source resources such as databases and tools to explore and analyze protein sequences and structures. A large part of the course will focus on the participant-led practical activities.

The schedule and materials for the course will be updated here: https://git.embl.de/sharan/protein-bioinformatics-nov-2016/blob/master/README.md

The preliminary content of the course:

Part-1: Protein databases and sequence analysis

– Protein databases: NCBI and UniProt
– Human protein atlas
– Antibodypedia
– EMBOSS toolkits
– Gene Ontology
– BLAST software package
– HMMER
– Multiple sequence alignments
– Jalview for motif visualization

Part-2: Protein structure analysis

– Secondary vs tertiary structure vs protein complexes
– PDB structure database
– Structure visualization by Chimera version-2
– Secondary and tertiary structure prediction
– Domain databases: InterPro, Pfam, SCOP etc.
– Intrinsically disordered region
– Eukaryotic Linear Motif (ELM)
– IUPRED
– Protein-protein interaction: STRING, BioGrid etc.
– Prediction of transmembrane helices in proteins

Part-3: Case study

– Participant-driven group activities
– Group presentations

Prerequisites:
– Basic knowledge of protein sequences and structures
– Interest in basic bioinformatics based analysis

Keywords:
Proteins, BLAST HMMER, PFAM

Tools:
BLAST, HMMER, different protein databases

Contact:
Malvika Sharan This email address is being protected from spambots. You need JavaScript enabled to view it.

Registration:
https://bio-it.embl.de/events/protein-bioinfo-2018/

Course Fee:
EMBL Bio-IT will offer the course for free for all EMBL members.

The external participants will be changed with a course fee of 90 Euros (to cover the lunch and infrastructure related cost). The invoice details will be shared via email.