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Analysis and prediction of carbohydrate binding sites.
- Source :
-
Protein engineering [Protein Eng] 2000 Feb; Vol. 13 (2), pp. 89-98. - Publication Year :
- 2000
-
Abstract
- An analysis of the characteristic properties of sugar binding sites was performed on a set of 19 sugar binding proteins. For each site six parameters were evaluated: solvation potential, residue propensity, hydrophobicity, planarity, protrusion and relative accessible surface area. Three of the parameters were found to distinguish the observed sugar binding sites from the other surface patches. These parameters were then used to calculate the probability for a surface patch to be a carbohydrate binding site. The prediction was optimized on a set of 19 non-homologous carbohydrate binding structures and a test prediction was carried out on a set of 40 protein-carbohydrate complexes. The overall accuracy of prediction achieved was 65%. Results were in general better for carbohydrate-binding enzymes than for the lectins, with a rate of success of 87%.
- Subjects :
- Algorithms
Amino Acids chemistry
Animals
Artificial Intelligence
Binding Sites
Databases, Factual
Enzymes chemistry
Enzymes metabolism
Humans
Immunoglobulin Fab Fragments chemistry
Immunoglobulin Fab Fragments metabolism
Lectins chemistry
Lectins metabolism
Ligands
Models, Chemical
Protein Binding
Protein Structure, Tertiary
Sequence Homology, Amino Acid
Solvents pharmacology
X-Ray Diffraction
Carbohydrate Metabolism
Carbohydrates chemistry
Proteins chemistry
Proteins metabolism
Subjects
Details
- Language :
- English
- ISSN :
- 0269-2139
- Volume :
- 13
- Issue :
- 2
- Database :
- MEDLINE
- Journal :
- Protein engineering
- Publication Type :
- Academic Journal
- Accession number :
- 10708647
- Full Text :
- https://doi.org/10.1093/protein/13.2.89