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README.md

|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: Malvika and Ben
    • NCBI (quick overview)
    • UniProt
      • Swissprot and Trembl
      • Cross-refrences and link-outs
        • OMIM, Domains, GO, ...
  2. Study of similar sequences: Marc
    • BLAST
      • BLASTp, BLASTn, PSI-BLAST, ...
    • Diamond
    • HHPred
    • HMMER
  3. Multiple sequence alignments: Malvika
    • 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

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

  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
    • SMART, SUPERFAMILY
    • Pfam
    • SCOP
  4. Prediction of transmembrane helices in proteins: Manjeet
    • TMHMM
  5. Intrinsically disordered region : Marc
    • ELM
    • IUPRED
    • DISPROT
  6. Protein-protein interaction: Michael
    • STRING and STITCH
    • Intact
    • 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