README.md

| Workshop| Protein bioinformatics for beginners| |----------|:-------------:|------:| |Dates|8 - 9 November| |Time|TBA| |Venue|ATC Computer lab, EMBL Heidelberg| |Trainers|Toby Gibson, Marc Gouw, Manjeet Kumar, Benjamin Lang, Malvika Sharan|

List of programs that we will cover in this workshop

Part-1 Protein databases and sequence analysis

1. Protein databases: Malvika
   • NCBI (quick overview)
   • UniProt
     • Swissprot
     • Cross-refrences and link-outs
       • OMIM, Domains, GO, ...
     • Trembl
2. Study of similar sequences: Marc
   • BLAST
     • BLASTp, BLASTn, PSI-BLAST,
   • HHPred
   • HMMER
3. Multiple sequence alignments: Ben
   • Muscle, Clustal omega, etc.
   • EMBOSS dot-plot
4. Other resources: Toby & Malvika
   • Human portein atlas
   • Antibodypedia
   • EMBOSS toolkits
   • Pepinfo
   • Sixpack
   • dotmatcher

Part-2 Protein structure analysis

• Toby's keynote: * Secondary vs tertiary structure vs protein complexes (Theory)

1. Protein Structures: Toby
   • Structure dtabase: PDB
   • Structure visualization
     • Chimera V2
   • Motif visualization
     • Jalview
     • MEME
     • Weblogo
2. Structure prediction: Malvika
   • jpred
   • Jalview linked tool Janet
   • PSIpred
   • Tertiary structure prediction: Phyre2, I-TASSER
3. Domain databases: Manjeet
   • InterPro & InterProScan
   • Pfam
   • SCOP
   • SMART, SUPERFAMILY
4. Prediction of transmembrane helices in proteins: Manjeet
   • TMHMM
5. Intrinsically disordered region : Marc
   • ELM
   • IUPRED
   • DISPROT
6. Protein-protein interaction: Malvika
   • STRING
   • BioGrid
   • MINT

Important references

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

Piratenpad link

- https://piratenpad.de/p/gibson_workshops