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  1. ArchDB
    Resource Category : Databases -> Structure Databases -> Protein structure

    Brief Description : ArchDB (http://sbi.imim.es/archdb) is a relational database of classified structural motifs, consisting of one loop plus its bracing secondary structures. Motifs have been classified using an improved version[1] of ArchType[2], an automated loop classification program. ArchType has been successfully applied to the SCOP95 set from SCOP 1.65 release[3]. The previous non-redundant classification[1], based on the SCOP40 set, has also been updated. Currently, the SCOP90-based classification contains 46894 motifs clustered into 2029 classes and 5111 subclasses, and the SCOP40-based classification contains 24356 motifs clustered into 1221 classes and 3575 subclasses. In addition, a manually curated classification of a subset of kinase proteins, ArchKI, has been included[4]. Functional annotations concerning residues found within clustered motifs has been incorporated into ArchDB, such as small ligand contacts (within 6.0 Å) and PDB SITE and ACTSITE records[5]. SCOP domain classification and protein functional descriptors such as EC numbers[6] and GO terms[7] are also reported. Subclasses displaying conserved functional or structural annotations (above 75%) are reported.

    Institute/s :
    Grup de Recerca d’Informatica Biomedica—IMIM, Spain
    Address of Institute/s :
    Grup de Recerca d’Informatica Biomedica—IMIM, Spain
    Country : Spain

    Associated Institutes :

    • Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica, Universitat Autonoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
    • Laboratori de Bioinformatica Estructural, Grup de Recerca d’Informatica Biomedica—IMIM, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, C/Doctor Aiguader 80, Barcelona 08003, Catalonia, Spain
    • Structural Bioinformatics Group, Biochemistry Building, Department of Biological Sciences, Imperial College, London SW7 2AZ, UK

    Associated Country : Spain; United Kingdom


    Authors/Contributors : Jordi Espadaler; Narcis Fernandez Fuentes; Antonio Hermoso; Enrique Querol; Francesc X. Aviles; Michael J. E. Sternberg; Baldomero Oliva
    Contact Email : boliva@imim.es
    Year : 2003
    Language : English