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URL: http://sbi.imim.es/cgi-bin/archdb/loops.pl

Proper Citation: ArchDB - Biological Database of Protein Loops (RRID:SCR_013472)

Description:
ArchDB is a compilation of structural classifications of loops extracted from known protein structures.
ArchDB includes 4 classifications:
* ArchDB40 contains the classification of loops extracted from proteins domains of ASTRAL SCOP with less that 40% sequence identity.
* ArchDB95 contains the classification of loops extracted from proteins domains of ASTRAL SCOP with less that 95% sequence identity.
* ArchDB-EC is a classification of loops extracted from proteins with known enzymatic function
* ArchDB-KI is a curated classification database of kinase loops EC number 2.7.X.X with functional information of residues.
Futhermore, the functional annotation of residues in this database are further classified in four categories:
1. ATP interaction: for residues involved on ATP binding/interaction.
2. Substrate binding: for residues involved in substrate interaction/binding with the exception of ATP
3. Ion interaction: for residues involved in ion interaction/binding of ions needed for the catalytic mechanism
4. Catalytic: involved in reaction, the stabilization of a transition state or the activation of substrates.
Additionally, three different approaches were applied to identify functional residues of the loops of the sub-classes:
1. Residues found within a cut-off distance of 6���� from an heteroatom, ligand, inhibitor, cofactor or complex partner molecule (protein or DNA), with the exception of D2O or crystallization buffer molecules.
2. Residues identified by functional information from ACTSITE and SITE records in the RCSB protein data bank.
3. Residues identified by the functional annotation collected from the literature and assigned to specific motifs of kinases.
Lastly, the multiple ways to browse and query in ArchDB are:
* Search by sequence: Users can search for classified loop(s) with sequence similarity to a query sequence.
* Search by structure: Users can upload protein coordinates in PDB format and its loops will be extracted and compared with those from the classification. First: structural class is assigned comparing loop geometry and, second: the loop conformation is compared among the subclasses within the assigned class.
* Search subclasses and/or Search Loops: A range of options are offered for subclass or loop searches. Users can query ArchDB asking for subclasses or loops with specific flanking secondary structures, length of loops or phi/psi loop conformation. Also, users can retrieve all subclasses or loops with PDB SITE annotations and contacts with co-crystallized ligands. Finally, users can search for subclasses that have SCOP, GO or EC annotations conserved at different percentage levels.
* Search structures: Users can search for classified PDB structures in ArchDB with specific Sprot. Annotation/Keyword, GO annotation, SCOP and EC codes.
* Specific queries for ArchDB-KI: Users can list functional subclasses or loops classified in ArchKI.
:Sponsors: ArchDB is funded by grants from Fundacin Areces (Spain), Ministerio de Ciencia y Tecnologa Spain (MCYT; BIO2002-03609, BIO2001-246 and BIO2001-264), Centre de Referncia en Biotecnologia Generalitat de Catalunya (CERBA), and the Generalitat de Catalunya
:
:Enzyme-specific classification,
:Kinase proteins, ligand, Protein residue, Protein motif, Protein loop,

Synonyms: ArchDB

Resource Type: data or information resource, database

Keywords: enzyme-specific classification, kinase proteins, ligand, protein loop, protein motif, protein residue, protein structure database

Resource Name: ArchDB - Biological Database of Protein Loops

Resource ID: SCR_013472

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