The numbered positions of annotated residues in the Swiss-Prot sequence often do not align to the same numbered positions of the sequence from the PDB structure. Therefore, a mapping of positions between the Swiss-Prot sequence and the PDB sequence must be obtained. We use a variation of the Needleman and Wunsch algorithm to identify if a sequence of a PDB structure can be found to match the sequence containing annotated residues from the Swiss-Prot database.
Specifically, every Swiss-Prot sequence containing one or more annotated residues and a link to a PDB structure was aligned to the corresponding sequence of the PDB structure. Standard annotations of Swiss-Prot used include post-translational modifications (MOD_RES), covalent binding of a lipid moiety (LIPID), glycosylation sites (CARBOHYD), post-translational formed amino acid bonds (CROSSLNK), metal binding sites (METAL), chemical group binding sites (BINDING), calcium binding regions (CA_BIND), DNA binding regions (DNA_BIND), nucleotide phosphate binding regions (NP_BIND), zinc finger regions (ZN_FING), enzyme activity amino acids (ACT_SITE) and any interesting single amino acid site (SITE). To ensure that the mapping is accurate, only alignments of two sequences with a sequence identity greater than ninety five percent were used. The annotated positions from Swiss-Prot are then transferred onto the PDB sequence, as long as the position is not aligned to a gap.
Specifically, every Swiss-Prot sequence containing one or more annotated residues and a link to a PDB structure was aligned to the corresponding sequence of the PDB structure. Standard annotations of Swiss-Prot used include post-translational modifications (MOD_RES), covalent binding of a lipid moiety (LIPID), glycosylation sites (CARBOHYD), post-translational formed amino acid bonds (CROSSLNK), metal binding sites (METAL), chemical group binding sites (BINDING), calcium binding regions (CA_BIND), DNA binding regions (DNA_BIND), nucleotide phosphate binding regions (NP_BIND), zinc finger regions (ZN_FING), enzyme activity amino acids (ACT_SITE) and any interesting single amino acid site (SITE). To ensure that the mapping is accurate, only alignments of two sequences with a sequence identity greater than ninety five percent were used. The annotated positions from Swiss-Prot are then transferred onto the PDB sequence, as long as the position is not aligned to a gap.
