Table 2

Non-validated functional annotations of non-annotated surface patches. Functional annotated sites have been compared to a collection of surface patches extracted from a non-redundant PDB subset. The reliability of each match was estimated via a series of criteria, as described in the text. The remaining similarities may be new functional annotations of uncharacterized functional sites, or false positive matches, and are shown in this table. Columns:(i) PDB code, chain name and patch number in the annotated query patch; (ii) Description of the protein to which the query patch belongs; (iii) Query patch functional annotation; (iv) Target patch; (v) Description of the protein to which the target patch belongs; (vi) Z-score of the match; (vii) SSM Q score; (viii) SSM P score; (ix) SSM Z score. The SSM Q score takes into account the number of aligned residues, their r.m.s.d. and the size of the proteins; a high Q score means a good similarity. The SSM P score is the log of the pValue (the probability that the match occurred by chance); P scores higher than 3 are considered significant by the authors of the method.

Ferrè et al. BMC Bioinformatics 2005 6:194   doi:10.1186/1471-2105-6-194