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