Prediction of specificity determining positions (SDPs) and physicochemical properties related to the functional specificity.

Florencio Pazos. (2021). Prediction of Protein Sites and Physicochemical Properties Related to Functional Specificity. Bioengineering 8(12):201.
[PubMed:34940354]

This directory contains additional examples of applications of the method (in supervised mode) to the families described at:

Florencio Pazos, Antonio Rausell & Alfonso Valencia. (2006). Phylogeny-independent detection of functional residues. Bioinformatics. 22(12):1440-1448. 

The *.txt files contain the results. Format:

 pos   aa      prop# propID                     CORR
  43    K   43    10 factor4     -  -1  xP    0.3726
  43    K   43     1 MW          -  -1  xP    0.3273
  55    Y   55    14 hdf_Eisenb  -  -1  xP    0.3061
  12    S   12    17 rel_mut     -  -1  xP    0.2889
  55    Y   55      -1   0.911   -  -1  xx    0.2795
  12    S   12     5 bulkiness   -  -1  xP    0.2788
....
..

pos           Position number in the alignment (numbering includes gaps). Take a 
              look at the corresponding  *.eq  file for the equivalences with the
              PDB numbers of the structure used to map the residues.
aa            Aminoacid of the first sequence in the alignment.
prop#         Index of the physicochemical property
propID        Name of the physicochemical property
              For the correlation with the amino-acid similarity matrix, these two
              are "-1" and entropy of the position respectively (see position 55
              in the example above). The entropy parameter quantifies que conservation 
              of that position (full cons. => entrop=0.0).
CORR          MAIN SCORE of the method.