SIFTS Mapping

SIFTS (Structure Integration with Function, Taxonomy and Sequences) provides an up-to-date resource for residue-level mapping between Uniprot and PDB entries. The information is updated and released weekly simultaneously with the release of new PDB entries. SIFTS Entries are published as XML files and made publicly available via an FTP site hosted at the European Bioinformatics Institute.

At the point of viewing a PDB structure, if the default mapping method is set as 'SIFTS', Jalview will download a SIFTS file for the target entry and uses it to accurately map the sequence residues with the structure residue. Prior to SIFTS integration, Jalview uses Needleman and Wunsch Alignment algorithm to map sequence residues to structure residues, and that may not always result to a correct mapping since it is computational determined.

Configuration
The default mapping method can be configured via Tools → Preferences → Structure tab Then scroll to the 'Sequence ↔ Structure method' section of the dialog box and change the default method. When 'SIFTS' is enabled as the default, all mappings between 'Sequence ↔ Structure' is performed via SIFTS provided that there is a valid SIFTS resource for the PDB entry. If no valid SIFTS resource is available, then the 'Sequence ↔ Structure' mapping falls back to Needleman and Wunsch Alignment algorithm.

Multi-Chain Mappings
One of the main merits of SIFTS is the ability to accurately achieve multi-chain mapping (one-to-many) between a single Uniprot sequence and its corresponding multiple chains in PDB. Consequently, mousing over the uniprot sequence in the alignment window results to highlighting multiple corresponding positions in the structure viewer for the mapped chains.

To see this in action, load uniprot sequence for FER1_MAIZE then veiw PDB structure for 3B2F, you will notice that mousing over the sequence results to two positions being highlighted in the structure, also colouring the sequence transfers the color to all the mapped chains in the structure.

Viewing Mapping Output
The mapping output is accessible via File → View mapping menu of the structure viewers. The screenshot below is the mapping output for the {FER1_MAIZE ↔ 3B2F} example described above. Observe that all the two chains were mapped. The mapping method used can be seen within the area highlighted with red boarder. This is useful for visually ascertaining the mapping method when in doubt.

SIFTS Mapping integration was added in Jalview 2.9.1