Diapo :
Functional :
- catalytic activity
- folding
- comunication
    - with partners
    - communication pathways (allostery, ...)
Environmental :
- cellular localisation (mitochondira, menbrane, ...)
- alone or in a complex

Discriminant :
- results from a different "history"
- markers of new adaptation
- may indicate new protein function ("moonlighting function")

Diapo :
Conservation and/or Variability scores
- define structural or functional residues
- define residues breaking evolution
- define differentially conserved residues
    -> new functions


Diapos :
Types of scores :
Symbol Frequency
Stereochemical property
Symbol Entropy
Stereochemically sensitive entropy
Substitution matrix
Phylogeny


Diapo :
Parameters :
- scoring function (89)
- sequence weighting (2)
- % of column completeness (5)
- clustering algorithm (3)
- group determination method (2)

Diapo :
Benchmark :

Catalytic Site Atlas (CSA) :
database documentating enzymes active sites and catalytic residues from 3D structures. Information manually extracted from origial litterature.

Prosite
Database of patterns / profiles defining a domain and/or function inside a protein sequence or a protein family sequences.
[KR]-[LIVM](2)-[GASL]-x-[GT]-x-[LIVMA]-x(2,5)-[LIVMF]-x-[LIVMF]-x(3,4)-[LIVMFCA]-[ST]-x(2)-A-x(3)-[LIVM]-x(3)-G

Pfam :
Database of multiple sequences alignments alignment (15648) and HMM of protein families.

Protocole :
- map PDB sequence onto Pfam alignment
- map Prosite motifs
- remove sequences having more than 95% of seq identity
- if nbr seq > 500, randomly sample to have 500.



Diapo :
Benchmark

Number of Pfam ...... : 813
mean/sd identity .... :  35.3/ 13.8
mean/sd length ...... : 539.9/339.0
mean/sd nbr seqs .... : 472.9/104.7

Total nbr columns ... : 302869
Nbr sites ........... : 4998


Diapo :
Global Results :

Sensibility
   | sensib specif power  | gapT ClusM 
 1 | 0.9306 0.7382 0.6688 | 0.01 'secator' Kabat
 2 | 0.8507 0.7959 0.6466 | 0.10 'secator' Kabat
 3 | 0.8069 0.7767 0.5836 | 0.70 'secator' Kabat RPCA
 4 | 0.8041 0.8038 0.6079 | 0.50 'secator' Kabat Norm
 5 | 0.7977 0.7955 0.5932 | 0.70 'secator' Kabat Norm
 6 | 0.7965 0.7944 0.5909 | 0.50 'secator' Kabat RPCA
 7 | 0.7953 0.8018 0.5971 | 0.25 'secator' Kabat RPCA
 8 | 0.7897 0.8296 0.6193 | 0.25 'secator' Kabat
 9 | 0.7841 0.8202 0.6043 | 0.01 'mm' Kabat
10 | 0.7805 0.8245 0.6050 | 0.25 'secator' Kabat Norm

Specificity
   | sensib specif power  | gapT ClusM 
 1 | 0.1499 0.9896 0.1394 | 0.01 'dpc' Valdar
 2 | 0.2055 0.9889 0.1944 | 0.01 'dpc' Wang
 3 | 0.1469 0.9875 0.1344 | 0.01 'secator' Valdar
 4 | 0.2659 0.9868 0.2527 | 0.01 'dpc' Capra
 5 | 0.1477 0.9861 0.1338 | 0.10 'dpc' Valdar
 6 | 0.1817 0.9860 0.1677 | 0.01 'dpc' Peivar
 7 | 0.2707 0.9857 0.2564 | 0.01 'dpc' Kabat Capra
 8 | 0.2149 0.9852 0.2001 | 0.01 'secator' Wang
 9 | 0.3701 0.9849 0.3551 | 0.01 'dpc' Thompson
10 | 0.3870 0.9849 0.3718 | 0.01 'dpc' SanderSP

Power
   | sensib specif power  | gapT ClusM 
 1 | 0.9306 0.7382 0.6688 | 0.01 'secator' Kabat
 2 | 0.7595 0.8881 0.6476 | 0.01 'secator' Kabat Norm
 3 | 0.8507 0.7959 0.6466 | 0.10 'secator' Kabat
 4 | 0.7601 0.8669 0.6270 | 0.01 'secator' Kabat RPCA
 5 | 0.7771 0.8467 0.6238 | 0.10 'secator' Kabat Norm
 6 | 0.7897 0.8296 0.6193 | 0.25 'secator' Kabat
 7 | 0.7723 0.8464 0.6187 | 0.50 'secator' Kabat
 8 | 0.7073 0.9044 0.6117 | 0.01 'secator' RPCA
 9 | 0.8041 0.8038 0.6079 | 0.50 'secator' Kabat Norm
10 | 0.6877 0.9196 0.6073 | 0.01 'secator' Norm


Diapo :
0 - 30 % Identity :
Sensibility
   | sensib specif power  | gapT ClusM 
 1 | 0.8980 0.7765 0.6745 | 0.01 'secator' Kabat
 2 | 0.8484 0.8043 0.6527 | 0.01 'mm' Kabat
 3 | 0.8240 0.7320 0.5560 | 0.10 'mm' Kabat
 4 | 0.8060 0.7222 0.5282 | 0.25 'mm' Kabat
 5 | 0.8017 0.8065 0.6082 | 0.10 'secator' Kabat
 6 | 0.7227 0.7391 0.4618 | 0.50 'mm' Kabat
 7 | 0.7083 0.7846 0.4929 | 0.10 'mm' Liu2
 8 | 0.7055 0.8314 0.5369 | 0.25 'secator' Kabat
 9 | 0.6803 0.8637 0.5440 | 0.25 'mm' Capra
10 | 0.6767 0.8038 0.4806 | 0.70 'secator' Kabat RPCA

Specificity
   | sensib specif power  | gapT ClusM 
 1 | 0.2364 0.9958 0.2321 | 0.01 'secator' Thompson
 2 | 0.2062 0.9942 0.2004 | 0.01 'secator' Ranganatan Thompson
 3 | 0.2198 0.9927 0.2126 | 0.01 'secator' Wang Thompson
 4 | 0.2435 0.9925 0.2360 | 0.10 'secator' Thompson
 5 | 0.2342 0.9920 0.2262 | 0.01 'secator' Ranganatan Wang
 6 | 0.2931 0.9919 0.2850 | 0.01 'secator' Capra Thompson
 7 | 0.2931 0.9916 0.2847 | 0.01 'secator' Entrop1 Thompson
 8 | 0.2320 0.9916 0.2237 | 0.01 'secator' Wang
 9 | 0.2155 0.9906 0.2061 | 0.01 'dpc' Valdar
10 | 0.2471 0.9906 0.2377 | 0.25 'secator' Thompson

Power
   | sensib specif power  | gapT ClusM 
 1 | 0.8980 0.7765 0.6745 | 0.01 'secator' Kabat
 2 | 0.8484 0.8043 0.6527 | 0.01 'mm' Kabat
 3 | 0.8017 0.8065 0.6082 | 0.10 'secator' Kabat
 4 | 0.8240 0.7320 0.5560 | 0.10 'mm' Kabat
 5 | 0.6624 0.8914 0.5538 | 0.10 'mm' Capra
 6 | 0.6149 0.9352 0.5501 | 0.01 'secator' Kabat Norm
 7 | 0.6128 0.9325 0.5453 | 0.01 'mm' Kabat Norm
 8 | 0.6803 0.8637 0.5440 | 0.25 'mm' Capra
 9 | 0.6070 0.9352 0.5422 | 0.01 'mm' Norm
10 | 0.5898 0.9510 0.5408 | 0.01 'mm' RPCA Capra


Diapo :
30 - 50 % Identity :
Sensibility
   | sensib specif power  | gapT ClusM 
 1 | 0.9493 0.7159 0.6652 | 0.01 'secator' Kabat
 2 | 0.8785 0.7903 0.6688 | 0.10 'secator' Kabat
 3 | 0.8535 0.7759 0.6294 | 0.70 'secator' Kabat RPCA
 4 | 0.8485 0.7996 0.6482 | 0.50 'secator' Kabat Norm
 5 | 0.8478 0.7876 0.6354 | 0.50 'secator' Kabat RPCA
 6 | 0.8446 0.7924 0.6370 | 0.70 'secator' Kabat Norm
 7 | 0.8417 0.7965 0.6382 | 0.25 'secator' Kabat RPCA
 8 | 0.8307 0.8057 0.6363 | 0.10 'secator' Kabat RPCA
 9 | 0.8296 0.8151 0.6447 | 0.25 'secator' Kabat Norm
10 | 0.8264 0.8330 0.6594 | 0.25 'secator' Kabat

Specificity
   | sensib specif power  | gapT ClusM 
 1 | 0.1390 0.9899 0.1289 | 0.01 'dpc' Valdar
 2 | 0.1979 0.9890 0.1869 | 0.01 'dpc' Wang
 3 | 0.3662 0.9876 0.3538 | 0.01 'dpc' Kabat
 4 | 0.1411 0.9870 0.1281 | 0.01 'secator' Valdar
 5 | 0.1333 0.9870 0.1203 | 0.10 'dpc' Valdar
 6 | 0.1329 0.9865 0.1194 | 0.25 'dpc' Valdar
 7 | 0.1693 0.9865 0.1558 | 0.01 'dpc' RPCA Valdar
 8 | 0.3966 0.9864 0.3830 | 0.01 'dpc' SanderSP
 9 | 0.3955 0.9864 0.3819 | 0.01 'dpc' Entrop1
10 | 0.1779 0.9864 0.1643 | 0.01 'dpc' Peivar

Power
   | sensib specif power  | gapT ClusM 
 1 | 0.8017 0.8731 0.6748 | 0.01 'secator' Kabat Norm
 2 | 0.8785 0.7903 0.6688 | 0.10 'secator' Kabat
 3 | 0.9493 0.7159 0.6652 | 0.01 'secator' Kabat
 4 | 0.8114 0.8495 0.6609 | 0.01 'secator' Kabat RPCA
 5 | 0.7731 0.8871 0.6603 | 0.01 'secator' RPCA
 6 | 0.8264 0.8330 0.6594 | 0.25 'secator' Kabat
 7 | 0.8149 0.8436 0.6585 | 0.50 'secator' Kabat
 8 | 0.8196 0.8362 0.6558 | 0.10 'secator' Kabat Norm
 9 | 0.7424 0.9083 0.6508 | 0.01 'secator' Norm
10 | 0.8485 0.7996 0.6482 | 0.50 'secator' Kabat Norm

Diapo :
50 - 100 % Identity :
Sensibility
   | sensib specif power  | gapT ClusM 
 1 | 0.9219 0.6780 0.5999 | 0.01 'secator' Kabat
 2 | 0.8947 0.7268 0.6214 | 0.50 'secator' Kabat Norm
 3 | 0.8711 0.7505 0.6216 | 0.10 'secator' Kabat Norm
 4 | 0.8711 0.7240 0.5951 | 0.25 'secator' Kabat RPCA
 5 | 0.8699 0.7286 0.5985 | 0.70 'secator' Kabat RPCA
 6 | 0.8674 0.7411 0.6085 | 0.70 'secator' Kabat Norm
 7 | 0.8637 0.7341 0.5978 | 0.50 'secator' Kabat RPCA
 8 | 0.8625 0.7735 0.6360 | 0.01 'secator' Kabat Norm
 9 | 0.8625 0.7400 0.6025 | 0.10 'secator' Kabat RPCA
10 | 0.8587 0.7385 0.5973 | 0.01 'secator' Kabat RPCA

Specificity
   | sensib specif power  | gapT ClusM 
 1 | 0.0843 0.9860 0.0703 | 0.10 'dpc' Valdar
 2 | 0.1078 0.9858 0.0936 | 0.01 'secator' Valdar
 3 | 0.0756 0.9855 0.0611 | 0.25 'dpc' Valdar
 4 | 0.0781 0.9854 0.0634 | 0.50 'dpc' Valdar
 5 | 0.0830 0.9853 0.0683 | 0.50 'secator' Valdar
 6 | 0.1673 0.9850 0.1523 | 0.01 'dpc' Capra
 7 | 0.0905 0.9849 0.0754 | 0.10 'dpc' Kabat Valdar
 8 | 0.0880 0.9849 0.0729 | 0.10 'secator' Valdar
 9 | 0.0756 0.9847 0.0603 | 0.70 'dpc' Valdar
10 | 0.1276 0.9845 0.1121 | 0.01 'dpc' Wang

Power
   | sensib specif power  | gapT ClusM 
 1 | 0.8625 0.7735 0.6360 | 0.01 'secator' Kabat Norm
 2 | 0.8315 0.7924 0.6239 | 0.10 'secator' Norm
 3 | 0.8240 0.7991 0.6231 | 0.01 'secator' Norm
 4 | 0.8389 0.7838 0.6227 | 0.10 'secator' Kabat
 5 | 0.8711 0.7505 0.6216 | 0.10 'secator' Kabat Norm
 6 | 0.8079 0.8136 0.6216 | 0.25 'secator' Kabat
 7 | 0.8947 0.7268 0.6214 | 0.50 'secator' Kabat Norm
 8 | 0.7968 0.8213 0.6181 | 0.50 'secator' Kabat
 9 | 0.8575 0.7527 0.6102 | 0.25 'secator' Kabat Norm
10 | 0.8092 0.7999 0.6091 | 0.01 'secator' RPCA Liu2



Diapo :
0 - 30 % Identity :

   | sensib specif power  | gapT ClusM 
Sensibility
 1 | 0.8980 0.7765 0.6745 | 0.01 'secator' Kabat
 2 | 0.8484 0.8043 0.6527 | 0.01 'mm' Kabat
 3 | 0.8240 0.7320 0.5560 | 0.10 'mm' Kabat
 4 | 0.8060 0.7222 0.5282 | 0.25 'mm' Kabat
 5 | 0.8017 0.8065 0.6082 | 0.10 'secator' Kabat

Specificity
 1 | 0.2364 0.9958 0.2321 | 0.01 'secator' Thompson
 2 | 0.2062 0.9942 0.2004 | 0.01 'secator' Ranganatan Thompson
 3 | 0.2198 0.9927 0.2126 | 0.01 'secator' Wang Thompson
 4 | 0.2435 0.9925 0.2360 | 0.10 'secator' Thompson
 5 | 0.2342 0.9920 0.2262 | 0.01 'secator' Ranganatan Wang

Power
 1 | 0.8980 0.7765 0.6745 | 0.01 'secator' Kabat
 2 | 0.8484 0.8043 0.6527 | 0.01 'mm' Kabat
 3 | 0.8017 0.8065 0.6082 | 0.10 'secator' Kabat
 4 | 0.8240 0.7320 0.5560 | 0.10 'mm' Kabat
 5 | 0.6624 0.8914 0.5538 | 0.10 'mm' Capra
 6 | 0.6149 0.9352 0.5501 | 0.01 'secator' Kabat Norm
 7 | 0.6128 0.9325 0.5453 | 0.01 'mm' Kabat Norm
 8 | 0.6803 0.8637 0.5440 | 0.25 'mm' Capra
 9 | 0.6070 0.9352 0.5422 | 0.01 'mm' Norm
10 | 0.5898 0.9510 0.5408 | 0.01 'mm' RPCA Capra


Diapo :
30 - 50 % Identity :

   | sensib specif power  | gapT ClusM 
Sensibility
 1 | 0.9493 0.7159 0.6652 | 0.01 'secator' Kabat
 2 | 0.8785 0.7903 0.6688 | 0.10 'secator' Kabat
 3 | 0.8535 0.7759 0.6294 | 0.70 'secator' Kabat RPCA
 4 | 0.8485 0.7996 0.6482 | 0.50 'secator' Kabat Norm
 5 | 0.8478 0.7876 0.6354 | 0.50 'secator' Kabat RPCA

Specificity
 1 | 0.1390 0.9899 0.1289 | 0.01 'dpc' Valdar
 2 | 0.1979 0.9890 0.1869 | 0.01 'dpc' Wang
 3 | 0.3662 0.9876 0.3538 | 0.01 'dpc' Kabat
 4 | 0.1411 0.9870 0.1281 | 0.01 'secator' Valdar
 5 | 0.1333 0.9870 0.1203 | 0.10 'dpc' Valdar

Power
 1 | 0.8017 0.8731 0.6748 | 0.01 'secator' Kabat Norm
 2 | 0.8785 0.7903 0.6688 | 0.10 'secator' Kabat
 3 | 0.9493 0.7159 0.6652 | 0.01 'secator' Kabat
 4 | 0.8114 0.8495 0.6609 | 0.01 'secator' Kabat RPCA
 5 | 0.7731 0.8871 0.6603 | 0.01 'secator' RPCA
 6 | 0.8264 0.8330 0.6594 | 0.25 'secator' Kabat
 7 | 0.8149 0.8436 0.6585 | 0.50 'secator' Kabat
 8 | 0.8196 0.8362 0.6558 | 0.10 'secator' Kabat Norm
 9 | 0.7424 0.9083 0.6508 | 0.01 'secator' Norm
10 | 0.8485 0.7996 0.6482 | 0.50 'secator' Kabat Norm


Diapo :
50 - 100 % Identity :

   | sensib specif power  | gapT ClusM 
Sensibility
 1 | 0.9219 0.6780 0.5999 | 0.01 'secator' Kabat
 2 | 0.8947 0.7268 0.6214 | 0.50 'secator' Kabat Norm
 3 | 0.8711 0.7505 0.6216 | 0.10 'secator' Kabat Norm
 4 | 0.8711 0.7240 0.5951 | 0.25 'secator' Kabat RPCA
 5 | 0.8699 0.7286 0.5985 | 0.70 'secator' Kabat RPCA

Specificity
 1 | 0.0843 0.9860 0.0703 | 0.10 'dpc' Valdar
 2 | 0.1078 0.9858 0.0936 | 0.01 'secator' Valdar
 3 | 0.0756 0.9855 0.0611 | 0.25 'dpc' Valdar
 4 | 0.0781 0.9854 0.0634 | 0.50 'dpc' Valdar
 5 | 0.0830 0.9853 0.0683 | 0.50 'secator' Valdar

Power
 1 | 0.8625 0.7735 0.6360 | 0.01 'secator' Kabat Norm
 2 | 0.8315 0.7924 0.6239 | 0.10 'secator' Norm
 3 | 0.8240 0.7991 0.6231 | 0.01 'secator' Norm
 4 | 0.8389 0.7838 0.6227 | 0.10 'secator' Kabat
 5 | 0.8711 0.7505 0.6216 | 0.10 'secator' Kabat Norm
 6 | 0.8079 0.8136 0.6216 | 0.25 'secator' Kabat
 7 | 0.8947 0.7268 0.6214 | 0.50 'secator' Kabat Norm
 8 | 0.7968 0.8213 0.6181 | 0.50 'secator' Kabat
 9 | 0.8575 0.7527 0.6102 | 0.25 'secator' Kabat Norm
10 | 0.8092 0.7999 0.6091 | 0.01 'secator' RPCA Liu2