Category:Research

To Dos

Research

1. How ESST is different from PAM and BLOSUM? (measurement should be 'Log Odd Ratio'?)
   
   1. How does 'Subst' really work? (Is the probability format based on each background distributions of ENV or total?)
      
   2. How to make 'PAM' or 'BLOSUM'?
2. Formalize the rate of amino acid substitution, say, Sub(a) = Sol(a)*1/Hbonds(a)*SS(a)
   1. how much each of ENVs affect (contribute) residue conservations?
3. Evolutionary Classification of Protein Structures using the structural profiles
   

Programming

1. FaceView
   1. Resmap highlighting a specified region (
      1. e.g. http://samul.bio.cc/pdb/2dwo/A/resmap?start=$start&end=$end
      2. http://samul.bio.cc/pdb/3bhu/jmol/?res_num=xx
   2. Colour residue by expected residue conservation score
   3. Enable selecting ENVs
   4. Pagination of keyword search in an elegant way
   5. Presenting alignment between pdb chain and swissprot from ResMap (Double-map)
      1. with annotations from uniprot feature and structural envrionments
   6. COSMIC mutations
2. How to PAML?

MISC.

1. Gamma distribution (Nei et al., 2001, PNAS)
2. XSLT [1], [2], [3]