Toby Gibson, Malvika Sharan, Marc Gouw, Manjeet Kumar, Michael Kühn (HD-HuB)
26/02/2018 - 28/02/2018
09:30 - 17:00
ATC Computer Training Lab
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 preliminary content of the course:
Part-1: Protein databases and sequence analysis
– Protein databases: NCBI and UniProt
– Human protein atlas
– EMBOSS toolkits
– Gene Ontology
– BLAST software package
– 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)
– Protein-protein interaction: STRING, BioGrid etc.
– Prediction of transmembrane helices in proteins
Part-3: Case study
– Participant-driven group activities
– Group presentations
– Basic knowledge of protein sequences and structures
– Interest in basic bioinformatics based analysis
Proteins, BLAST HMMER, PFAM
BLAST, HMMER, different protein databases
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.