| 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