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Table 7 Assessment of different methods.

From: Combining specificity determining and conserved residues improves functional site prediction

Family ET Rate4site FASS MB S
PF00108 C C - - no MW
PF00128 - ++C n/a n/a n/a
PF00135 - - n/a n/a n/a
PF00215 - ++ no MW - no MW
PF00278 + +C - - no MW
PF00293 ++C + n/a n/a n/a
PF00303 C C no MW + 0
PF00348 ++C ++C - ++C -
PF00351 + + n/a n/a n/a
PF00579 ++ ++ - +C no MW
PF00583 - - n/a n/a n/a
PF00590 ++ ++ no MW - -
PF00693 +C +C n/a n/a n/a
PF00755 ++C ++C n/a n/a n/a
PF00871 ++C ++C n/a n/a n/a
PF00896 + - n/a n/a n/a
PF00925 C C 0 - 0
PF00962 ++C +C no MW ++C C
PF01014 ++C ++C no MW ++C 0
PF01048 +C +C - - -
PF01112 - + n/a n/a n/a
PF01135 ++ ++ n/a n/a n/a
PF01202 - - no MW + 0
PF01227 + - - - 0
PF01234 +C +C n/a n/a n/a
PF01293 +C C n/a n/a n/a
PF01467 - - 0 - 0
PF01583 - - no MW - 0
PF01656 ++C ++C no MW - no MW
PF01702 ++ ++ n/a n/a n/a
PF01712 ++C C n/a n/a n/a
PF01747 ++C ++C ++C ++C -
PF02110 ++C +C n/a n/a n/a
PF02223 ++C + no MW - 0
PF02274 ++C ++C - C -
PF02277 C C no MW - 0
PF02353 ++ ++ n/a n/a n/a
PF02569 ++C C n/a n/a n/a
PF02898 - + n/a n/a n/a
PF02901 ++ ++ n/a n/a n/a
PF03061 - - 0 - 0
PF03171 - - no MW - 0
PF03332 - - n/a n/a n/a
PF03414 ++C +C n/a n/a n/a
Success rate 32/44 34/44 1/7 8/22 1/5
  1. ET: evolutionary trace method [13, 14]; ConSurf: ConSurf method [9]; FASS, MB, S: three methods from the TreeDet package [32]. '++': SDPsite with both λ = 0.5 and λ = 1 performs significantly better (p-value < 0.01 in Mann-Whitney test), '+': SDPsite with either λ = 0.5 or λ = 1 performs significantly better, 'C': SDPsite with CPs only performs significantly better; 'n/a' method is not applicable, 'no MW': Mann-Whitney test is unreliable (less than 5 value in one of the sets), 0: method applicable, but no positions predicted, prediction considered not successful.