Protein Structure and Function. Application of Bioinformatics Methods - John Rigden 2014

Integrated servers for structure-based function prediction
ProKnow
Structural motifs

Following the matching fold search stage, the 3D Structure OF THE protein is scanned for any Structural Motifs directly related to its function. Such motifs are stored in the RIGOR database of automatically generated structural motifs (Kleywegt 1999). Each motif consists of an "interesting" arrangement of residues within the PDB structure. Three rules are used to distinguish interesting residues from uninteresting ones: (a) the protein contains n consecutive residues of the same type (for example, four consecutive Arginine residues), (b) a series of neighboring residues is entirely hydrophobic, polar/charged, or a combination of hydrophobic and polar/charged, and (c) all residues are in contact with a single heterocompound. ProKnow utilizes over 10,000 motifs from the RIGOR database, each associated with a GO term for the corresponding protein chain.



Last update: 06/08/2026

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