|Workshop|Protein bioinformatics for beginners| |----------|:-------------:|------:| |Dates|8 - 9 November| |Time|09:30 - 17:00 hrs| |Venue|ATC Computer lab, EMBL Heidelberg| |Trainers|Toby Gibson, Marc Gouw, Michael Kuhn, Manjeet Kumar, Benjamin Lang, Malvika Sharan|

List of resources that will be covered in this workshop

Part-1 Protein databases and sequence analysis

1. Protein databases:
   • Introduction to protein databases: Malvika
   • Quick overview of NCBI: Malvika
   • UniProt: Ben
     • Swissprot and Trembl
     • Cross-refrences and link-outs
       • OMIM, Domains, GO, ...
2. Study of similar sequences: Marc
   • BLAST
     • BLASTp, BLASTn, PSI-BLAST, ...
   • Diamond
   • HMMER
   • HHPred
3. Multiple sequence alignments: Malvika
   • Clustal omega (EMBL-EBI)
   • COBALT (NCBI)
4. Other resources
   • Human Protein Atlas: Toby
   • Antibodypedia: Toby
   • EMBOSS toolkits: Malvika
     • EMBOSS explorer
     • Alignment and plotting tools
       • dotmatcher

Part-2 Protein structure analysis

Lecture (Toby): Secondary vs tertiary structure vs protein complexes

1. Protein Structures: Toby
   • Structure database: PDB at RCSB
   • Structure visualization
     • Chimera
2. Structure prediction: Malvika
   • jpred: Jalview
   • Tertiary structure prediction: Phyre2, I-TASSER
3. Domain databases: Manjeet
   • SMART
   • Pfam
   • Superfamily
   • InterPro & InterProScan
4. Prediction of transmembrane helices in proteins: Manjeet
   • TMHMM
   • IUPRED and Anchor
5. Intrinsically disordered region: Marc
   • ELM
   • DISPROT
6. Protein-protein interaction: Michael
   • STRING and STITCH
   • Intact
   • MINT
7. Motif visualization:
   • Weblogo (Malvika)
   • MEME (Malvika)
   • Jalview Alignment Viewer (Toby)

Important references

- http://www.sciencedirect.com/science/book/9788131222973
- http://molbiol-tools.ca/Protein_Chemistry.htm
- http://www.ebi.ac.uk/Tools/pfa/

Post workshop survey