5 <title>SIFTS Mapping from UniProt for PDB Structures</title>
10 <strong>SIFTS Mapping for UniProt sequences and PDB
11 Structures</strong><br /> SIFTS (Structure Integration with Function,
12 Taxonomy and Sequences) is a database of residue-level mappings
13 between UniProt protein sequences, and protein structures found in
14 the PDB. The database is updated for each PDB release, and is
15 provided by the <a href="https://www.ebi.ac.uk/pdbe/docs/sifts/">PDBe
18 <p>When Jalview imports PDB data for a protein sequence found in
19 UniProt, either via the 'View 3D Structure...' option, or the 'Fetch
20 DB Refs' web services menu, Jalview will also download its SIFTS
21 record and use that information to construct a mapping between the
22 sequence and downloaded structure.</p>
23 <p>If, for some reason, no SIFTS mapping data exists, then Jalview
24 will generate a mapping using the built-in Needleman and Wunsch
25 global alignment algorithm. This is how sequence-structure mappings
26 were created before version 2.10.</p>
27 <p><strong>Controlling and troubleshooting SIFTS mappings</strong> <br />
28 Configuration options controlling whether SIFTS mappings are used
29 can be found in the <strong>Tools → Preferences →
30 Structure tab</strong>, under 'Sequence ↔ Structure method'.<br /> <em>Note:</em>
31 Changing the configuration will only affect how new mappings are
32 created. In order to recompute mappings for structures already
33 loaded, please reload the sequence & structural data.
37 <strong>Multi-Chain Mappings</strong> <br />SIFTS gives Jalview the
38 ability to display multi-chain mappings between UniProt sequences
39 and PDB structure data. This is important when working with
40 multimeric proteins, when the biological assembly can contain several
41 structures for the same protein sequence. Multi-chain mapping allows
42 all residues in a structure to be located in the alignment, and
43 also, when shading the structure by sequence colours, enables
44 conservation patterns between oligomer interfaces to be explored.
46 <p>To see this in action, Retrieve the UniProt sequence
47 FER1_MAIZE, and then view one of its structures: 3B2F. Mousing over
48 the sequence results to two positions being highlighted in the
49 structure, and colouring the alignment transfers the color to all
50 the mapped chains in the structure.</p>
53 <Strong>Viewing Mapping Output</Strong> <br /> The mapping provided
54 by the SIFTS record is accessible via <strong>File →
55 View mapping</strong> menu of the structure viewers. The screenshot below
56 shows the mapping created between UniProt sequence FER1_MAIZE and proteins in PDB 3B2F, which reports thattwo chains
57 were mapped. The mapping method is also reported (highlighted with red border).
60  <img src="sifts_mapping_output.png" align="left"
61 alt="SIFTS mapping output" />
64 <em>SIFTS Mapping integration was added in Jalview 2.10</em>