Domains are the evolutionary, structural and functional units of proteins. Nevertheless, current annotations of molecular functions are done on a whole-chain basis, without associating specific molecular functions to the individual domains. Even domain-oriented databases suffer from this problem. This can cause troubles in many studies of domains from a functional point of view.
The Scop2go resource was created with the aim of generating the first database of domain-oriented functional annotations. The initial set of annotations were obtained by a fully-automatic procedure for discerning which structural domain within a chain is responsible for a given GO molecular function term originally associated to the whole chain (Lopez & Pazos, 2009). The method is based on the fold distribution of the set of PDB chains associated to a given GO molecular function term. Applying this method to the whole-chain-based annotations of PDB chains generated by the GOA-PDB project, annotations were obtained for their structural domains as defined in SCOP.
Currently scop2go contains annotations for 47229 SCOP domains (and groups of domains) belonging to 37923 PDB chains using 1297 GO molecular function specific terms.
This initial set of functional annotations automatically obtained can be the basis for a future manually curated set of annotations such as the ones available for whole-chains. One of the goals of the Scop2go resource is to correct and extend this initial set of annotations with the help of the community in a sort of collaborative or wiki-like project. This web site allows not only to query the current annotations, but also to suggest corrections or additional annotations.
Help on using scop2go
Entries in the database are accessed either by the Gene Ontology term, by the SCOP sid identifier, or by the PDB code, as well as a part of them. Non-alphanumeric character are not allowed. For example, valid searches are "1jny", "1jnyA1", "bmt", "GO:0050897", etc.
The results include the SCOP domains matching the search criteria as well as the corresponding complete chains. This is because the results of the method assigning GO terms to domains have to be always interpreted in the context of the terms originally associated to the corresponding whole chains. Terms not associated to the complete chain will never be (automatically) assigned to the domains.
The GO terms originally associated to the complete chains and the ones assigned to the individual domains are shown. PDB chains, structural domains and GO terms are linked to the corresponding web pages in PDBSUM, SCOP and GeneOntology respectively. Only specific terms are included in the lists. Their ancestors (less specific terms) can be obtained with the button.
Besides the functional annotations for a given structural domain, there is a link () for visualizing that domain in the 3D structure of the corresponding chain with the Jmol applet. Additionally, a symbol indicates whether that annotation was automatically obtained () or manually curated (). For automatic annotations, a p-value associated to that automatic prediction is also shown (see reference above).
Finally, a "suggest correction" link () takes the user to a form which can be used for suggesting corrections, changes and new annotations to the database administrators. To keep this as simple as possible, these corrections are provided as free-text. Nevertheless, a template for writing these suggestions is included. Any suggested functional annotation should include the GO id of the functional term as well as an explanation for the proposed chage/addition, and a bibliographic reference(s) or similar supporting that.
Automatically linking to Scop2Go
Constructing URLs pointing to the annotations in Scop2go is easy. They should be in the form:
http://pdg.cnb.csic.es/scop2go/search.jsp?search=XXXXwhere XXXX is a valid SCOP sid, PDB or GO term (see avobe). For example:
Daniel Lopez & Florencio Pazos
Computational Systems Biology Group (CNB-CSIC)
For questions/comments on this server, please contact Daniel Lopez:
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