diff --git a/README.md b/README.md index b6b509ed613460aa2522bb2966e85c832b2425b2..0c7bd42cc12c65e00e10e0ef45e27c7b9e764314 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,16 @@ # Protein bioinformatics for beginners -## Schedule - -7 - 9 November, ATC Computer lab +## Dates: 8 - 9 November +## Time: TBA +## Venue: ATC Computer lab, EMBL Heidelberg +## Trainers: Toby Gibson, Marc Gouw, Manjeet Kumar, Benjamin Lang, Malvika Sharan ## Program **Part-1 Protein databases and sequence analysis** 1. Protein databases: Malvika - - NCBI (very quick overview) + - NCBI (quick overview) - UniProt - Swissprot - Cross-refrences and link-outs @@ -20,46 +21,53 @@ - BLASTp, BLASTn, PSI-BLAST, - HHPred - HMMER -3. Multiple sequence alignments: Manjeet - - UniProt aligner +3. Multiple sequence alignments: Ben + - Muscle, Clustal omega, etc. - EMBOSS dot-plot - - Muscle, Clustal omega 4. Other resources: Toby & Malvika - Human portein atlas - Antibodypedia - EMBOSS toolkits - - Pepinfo - - Sixpack - - dotmatcher: http://emboss.bioinformatics.nl/cgi-bin/emboss/dotmatcher - - Prediction of transmembrane helices in proteins: (This is a bit misplaced) - TMHMM (http://www.cbs.dtu.dk/services/TMHMM/) + - Pepinfo + - Sixpack + - dotmatcher **Part-2 Protein structure analysis** * Toby's keynote: * Secondary vs tertiary structure vs protein complexes (Theory) -1. Structure database: Toby - - PDB (http://www.rcsb.org/pdb/home/home.do) -2. Structure visualization: Toby - - Motif visualization: - - Jalview, MEME, Weblogo, Chimera (https://screenshots.debian.net/package/chimera2) -3. Structure prediction: ??? - - jpred (http://www.compbio.dundee.ac.uk/jpred/) - - Jalview linked tool Janet (?) - - PSIpred (?) - - Tertiary structure prediction - - I-TASSER -4. Domain databases: Ben - - InterPro, +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? + - SMART, SUPERFAMILY +4. Prediction of transmembrane helices in proteins: Manjeet + - TMHMM 5. Intrinsically disordered region : Marc - - ELM ( http://elm.eu.org) - - IUPRED (http://iupred.enzim.hu) - - DISPROT? + - ELM + - IUPRED + - DISPROT 6. Protein-protein interaction: Malvika - - STRING (http://string-db.org) - - BioGrid? - - MINT? + - STRING + - BioGrid + - MINT + +### 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 \ No newline at end of file