Documentation for the eFamily Schema

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Documentation for DAS alignment and DAS structure services

Version:1.0

Last Modification:03-Feb-2006 12:55:34

Authors: Andreas Prlic (ap3), Rob Finn, Thomas Down

Background

So far DAS (up to v1.5) has been used mainly to serve DNA data. To use if for proteins a couple of extensions are required. This document is specifying these extensions:

• a service that allows to communicate alignments
• a service that provides protein structure data
• an update of the entry_point service

Note: Many properties of proteins can already now be communicated using the feature service.

When working with proteins the coordinate system used is much more complicated than the one used for DNA assemblies. e.g.:

first line: A protein as it is contained within SwissProt/UniProt.

second line: The SEQRES protein sequences, which is contained in a PDB file, can be different to some extent. Here it does not provide some residues from the N terminus and contains a mutation.

third line: Actually it was only possible to obtain coordinates for these amino acid residues. The protein has some homology to another protein, so the numbering of the homologous one was chosen for the PDB file. PDB file numbering can be quite arbitrary. There can be negative positions, the order of the numbers does not need to be linear, there are alternative locations possible (indicated by "A", "B"), etc... Although being so complicated the PDB file numbering is still and important "standard" for the protein structure community. In future features of protein structures will be served using this "coordinate system"! To make the it a little easier, servers can obtain the mapping of PDB to Uniprot from MSD (link will be available here at some point). For each object that is communicated using DAS it is important to provide the coordiante system.

fourth line: MSD is renumbering the residues to their own coordinate system.

New services

The following new or modified services are being used by the SPICE - DAS client:

New services
Capability Name Description alignment/1.1 The server supports the basic alignment request. structure/1.0 The server supports the basic structure request. entry_points/1.1 (update of old capability)The server supports the basic entry_points request.

All orientation arguments that are used in various services are becoming optional, since orientation is related to the orientation along the DNA and is not needed for proteins.

To get a list of available alignments an alignment server should be queried using the entry_points request. The same applies to a structure server where entry_points returns the list of available chains and models. The previously depreciated argument ref of entry_points is re-established again.

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The Queries

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• alignment
• structure
• entry_points

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The XML schemes proposed on this site are also part of the eFamily XML scheme at http://www.efamily.org.uk/xml/efamily/documentation/efamily.shtml.

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The improvements in the DAS protocol allow new clients to be implemented. The SPICE client can be accessed at: http://www.efamily.org.uk/software/dasclients/spice/