|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
- Protein databases: Malvika and Ben
- NCBI (quick overview)
- UniProt
- Swissprot and Trembl
- Cross-refrences and link-outs
- OMIM, Domains, GO, ...
- Study of similar sequences: Marc
- BLAST
- BLASTp, BLASTn, PSI-BLAST, ...
- Diamond
- HHPred
- HMMER
- BLAST
- Multiple sequence alignments: Malvika
- Muscle, Clustal omega, etc.
- EMBOSS dot-plot
- 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
- Protein Structures: Toby
- Structure dtabase: PDB
- Structure visualization
- Chimera V2
- Motif visualization
- Jalview
- MEME
- Weblogo
- Structure prediction: Malvika
- jpred
- Jalview linked tool Janet
- PSIpred
- Tertiary structure prediction: Phyre2, I-TASSER
- Domain databases: Manjeet
- InterPro & InterProScan
- SMART, SUPERFAMILY
- Pfam
- SCOP
- Prediction of transmembrane helices in proteins: Manjeet
- TMHMM
- Intrinsically disordered region : Marc
- ELM
- IUPRED
- DISPROT
- 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