Discarding Functional Residues from the Substitution Table Improves Predictions of Active Sites within Three-Dimensional Structures
Figure 1
Probabilities of Residue Conservation for 21 Amino Acids.
The probability of residue conservation (PCONS) was averaged for the diagonal axis of substitution tables. (A) PCONS of three matrix-types (ENZ, NOENZ and ALL) are compared with the OLD. Non-masking models (X) were used for three matrix-types and OLD to see the effect of alignment source. (ENZ: enzyme-specific 221 SCOP families, NONENZ: non-enzymes, ALL: all the alignments, OLD: non-masking ESST of Shi et al. [11]. See Table 2 for details.) (B) Five masking tables and one non-masking table are compared with the ESST of Shi et al. [11]. Masking and non-masking tables are from the 221 enzyme-specific alignments (ENZ). Masking sources of A, B, C, and D are listed in Table 1. (R: random-masking, X: non-masking.)