Task 6 - EVfold
For the proteins used in this practical, structures have been determined. However, in real-life projects, you often do not have protein structures only sequences. During this practical, you already predicted secondary structure elements
correlated mutations
your protein
+ example P01112 (RASH_HUMAN)
http://pfam.sanger.ac.uk/family/Ras
calculating the evolutionary couplings
0. aligment (clustalw.... Pfam alignment good) Many sequences
1. a2m2lm.... => aligment 2. freecontact -> standard (installed on student computers)
Output -> all couplings + evolutionary coupling score (last column)
rank by score => look at distrubution, values, range
Meaning of score unclear
Take only scores for i+6, i.e. neighboring residues neglected, minimal 5 residues between coupled residues
Take ranking, check for each coupled pair the actual distance in the structure. TP: distance <= 5 AA (minimal distance of all pairs of all atoms of both residues)
EVcoupling
Check evolutionary hot spots, i.e. relevant residues, functionally important sites.
Take L couplings (L=length of protein sequence), sum scores for each residue. Analyze.
(Cell paper)
- compare to conservation, single site conservation
EVfold.org
create model
choose number of contacts: optimum ~ 60-70% of L 40% of L 100% of L
=> RMSD will be calculated by server, if you give PDB ID
PLM