An empirical approach for structure‐based prediction of carbohydrate‐binding sites on proteins

A computer program system was developed to predict carbohydrate‐binding sites on three‐dimensional (3D) protein structures. The programs search for binding sites by referring to the empirical rules derived from the known 3D structures of carbohydrate–protein complexes. A total of 80 non‐redundant ca...

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Bibliographic Details
Published in:Protein engineering 2003-07, Vol.16 (7), p.467-478
Main Authors: Shionyu‐Mitsuyama, Clara, Shirai, Tsuyoshi, Ishida, Hirokazu, Yamane, Takashi
Format: Article
Language:English
Subjects:
Animals
Binding Sites
Carbohydrate Metabolism
computer application/drug design/ligand prediction/molecular interaction/sugar
Databases, Protein
Humans
polysaccharides
Protein Binding
Protein Structure, Tertiary
Proteins - chemistry
Proteins - metabolism
Sequence Analysis, Protein
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Summary:A computer program system was developed to predict carbohydrate‐binding sites on three‐dimensional (3D) protein structures. The programs search for binding sites by referring to the empirical rules derived from the known 3D structures of carbohydrate–protein complexes. A total of 80 non‐redundant carbohydrate–protein complex structures were selected from the Protein Data Bank for the empirical rule construction. The performance of the prediction system was tested on 50 known complex structures to determine whether the system could detect the known binding sites. The known monosaccharide‐binding sites were detected among the best three predictions in 59% of the cases, which covered 69% of the polysaccharide‐binding sites in the target proteins, when the performance was evaluated by the overlap between residue patches of predicted and known binding sites.
ISSN:0269-2139
1741-0126
1460-213X
1741-0134
DOI:10.1093/protein/gzg065