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-<html>
-<head>
-<meta charset="UTF-8">
-<title>SIFTS Mapping from UniProt for PDB Structures</title>
-</head>
-<body>
-
- <p>
- <strong>SIFTS Mapping for UniProt sequences and PDB
- Structures</strong><br /> SIFTS (Structure Integration with Function,
- Taxonomy and Sequences) is a database of residue-level mappings
- between UniProt protein sequences, and protein structures found in
- the PDB. The database is updated for each PDB release, and is
- provided by the <a href="https://www.ebi.ac.uk/pdbe/docs/sifts/">PDBe
- at EMBL-EBI</a>.
- </p>
- <p>When Jalview imports PDB data for a protein sequence found in
- UniProt, either via the 'View 3D Structure...' option, or the 'Fetch
- DB Refs' web services menu, Jalview will also download its SIFTS
- record and use that information to construct a mapping between the
- sequence and downloaded structure.</p>
- <p>If, for some reason, no SIFTS mapping data exists, then Jalview
- will generate a mapping using the built-in Needleman and Wunsch
- global alignment algorithm. This is how sequence-structure mappings
- were created before version 2.10.</p>
- <p>
- <strong>Controlling and troubleshooting SIFTS mappings</strong> <br />
- Configuration options controlling whether SIFTS mappings are used
- can be found in the <strong>Tools → Preferences →
- Structure tab</strong>, under 'Sequence ↔ Structure method'.<br /> <em>Note:</em>
- Changing the configuration will only affect how new mappings are
- created. In order to recompute mappings for structures already
- loaded, please reload the sequence & structural data.
- </p>
-
- <p>
- <strong>Multi-Chain Mappings</strong> <br />SIFTS gives Jalview the
- ability to display multi-chain mappings between UniProt sequences
- and PDB structure data. This is important when working with
- multimeric proteins, when the biological assembly can contain
- several structures for the same protein sequence. Multi-chain
- mapping allows all residues in a structure to be located in the
- alignment, and also, when shading the structure by sequence colours,
- enables conservation patterns between oligomer interfaces to be
- explored.
- </p>
- <p>To see this in action, Retrieve the UniProt sequence
- FER1_MAIZE, and then view one of its structures: 3B2F. Mousing over
- the sequence results to two positions being highlighted in the
- structure, and colouring the alignment transfers the color to all
- the mapped chains in the structure.</p>
-
- <p>
- <Strong>Viewing Mapping Output</Strong> <br /> The mapping provided
- by the SIFTS record is accessible via <strong>File →
- View mapping</strong> menu of the structure viewers. The screenshot below
- shows the mapping created between UniProt sequence FER1_MAIZE and
- proteins in PDB 3B2F, which reports mappings for two chains. The
- mapping method is also reported (highlighted with red border).
- <p>
-
-  <img src="sifts_mapping_output.png" align="left"
- alt="SIFTS mapping output" /> <br />
- <p>
- <em>SIFTS Mapping integration was added in Jalview 2.10</em>
- </p>
-
-</body>
-</html>
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