diff --git a/README.md b/README.md index aa0abf968ee7c5edc97210bc795e61b4c8b02a49..b6b509ed613460aa2522bb2966e85c832b2425b2 100644 --- a/README.md +++ b/README.md @@ -6,4 +6,60 @@ ## Program -For now, please check the Piraten Pad: https://piratenpad.de/p/gibson_workshops \ No newline at end of file +**Part-1 Protein databases and sequence analysis** + +1. Protein databases: Malvika + - NCBI (very 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: Manjeet + - UniProt aligner + - 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/) + +**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, + - Pfam + - SCOP + - SMART? + - SUPERFAMILY? +5. Intrinsically disordered region : Marc + - ELM ( http://elm.eu.org) + - IUPRED (http://iupred.enzim.hu) + - DISPROT? +6. Protein-protein interaction: Malvika + - STRING (http://string-db.org) + - BioGrid? + - MINT?