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CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation.

(2010) BMC Bioinformatics 11

PubMed: 20796320 | PubMedCentral: PMC2936402 | DOI: 10.1186/1471-2105-11-439

The ROC curve of the CMASA, the FFF and the SPASM using the 1mct active site (H57, D102 and S195) searching to the nrSCOP.

The catalytic sites (H57, D102 and S195) of 1mct (a typsin) were used as the query to search against nrSCOP database, and the Receiver Operating Characteristics (ROC) curve[ 26 ] (Figure 4 ) is obtained.

The ROC curves were generated by 1mct active site (H57, D102 and S195) querying to nrSCOP using CMASA.

We also used the active sites of 1mct to search PINTS SCOP_specials database (SCOP version 1.61), 4 of 54 trypsins and 4 of 10 subtilisins can be hit.

The CMASA_RMSD was calculated between 1mct active site (H57, D102 and S195) and the hits by the CMASA.

The superposition results of the protein ( 1mct ) searching against the nrCSA database are shown in the Figure 2A , and the results of the active sites of 1mct (H57, D102, S195) searching against the nrPDB are shown in the Figure 2B .

A: a structure (pdbid: 1mct ) searched to a functional sites database (nrCSA); highest five ranks were shown.

Another case is to find trypsins and subtilisins by 1mct active sites (Figure 7B ).

B: a functional site ( 1mct catalytic site: H57, D102 and S195) searched to the nrPDB; the hits with P-value < 1.0 × 10 -4 were shown (83 hits).

The ROC curve shows that all of these three methods can hold the good performance, when they are used to detect the 1mct active site similarities (Figure 7B ), but some differences can be also observed.

For example, there are 135 candidates for emulating all H-D-S possible active sites in 1mct , a member of trypsin.

Publication Year: 2010