CAMPASS: a database of structurally aligned protein superfamilies
نویسندگان
چکیده
منابع مشابه
The FSSP database of structurally aligned protein fold families.
FSSP (families of structurally similar proteins) is a database of structural alignments of proteins in the Protein Data Bank (PDB). The database currently contains an extended structural family for each of 330 representative protein chains. Each data set contains structural alignments of one search structure with all other structurally significantly similar proteins in the representative set (r...
متن کاملProtein three-dimensional structural databases: domains, structurally aligned homologues and superfamilies.
This paper reports the availability of a database of protein structural domains (DDBASE), an alignment database of homologous proteins (HOMSTRAD) and a database of structurally aligned superfamilies (CAMPASS) on the World Wide Web (WWW). DDBASE contains information on the organization of structural domains and their boundaries; it includes only one representative domain from each of the homolog...
متن کاملDefining and predicting structurally conserved regions in protein superfamilies
MOTIVATION The structures of homologous proteins are generally better conserved than their sequences. This phenomenon is demonstrated by the prevalence of structurally conserved regions (SCRs) even in highly divergent protein families. Defining SCRs requires the comparison of two or more homologous structures and is affected by their availability and divergence, and our ability to deduce struct...
متن کاملSMoS: a database of structural motifs of protein superfamilies.
The Structural Motifs of Superfamilies (SMoS) database provides information about the structural motifs of aligned protein domain superfamilies. Such motifs among structurally aligned multiple members of protein superfamilies are recognized by the conservation of amino acid preference and solvent inaccessibility and are examined for the conservation of other features like secondary structural c...
متن کاملFrequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function.
Gap penalty is an important component of the scoring scheme that is needed when searching for homologous proteins and for accurate alignment of protein sequences. Most homology search and sequence alignment algorithms employ a heuristic 'affine gap penalty' scheme q + r x n, in which q is the penalty for opening a gap, r the penalty for extending it and n the gap length. In order to devise a mo...
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ژورنال
عنوان ژورنال: Structure
سال: 1998
ISSN: 0969-2126
DOI: 10.1016/s0969-2126(98)00110-5