A procedure for detecting structural domains in proteins.
A procedure is described for detecting domains in proteins of known structure. The method is based on the intuitively simple idea that each domain should contain an identifiable hydrophobic core. By applying the algorithm described in the companion paper (Swindells MB, 1995, Protein Sci 4:93-102) to identify distinct cores in multi-domain proteins, one can use this information to determine both the number and the location of the constituent domains. Tests have shown the procedure to be effective on a number of examples, even when the domains are discontinuous along the sequence. However, deficiencies also occur when hydrophobic cores from different domains continue through the interface region and join one another.
Swindells
M B
MB
Protein Engineering Research Institute, Osaka, Japan.
D000154:Aconitate Hydratase / Q000737:chemistry; D000426:Alcohol Dehydrogenase / Q000737:chemistry; D000465:Algorithms; D000595:Amino Acid Sequence; D001219:Aspartate Aminotransferases / Q000737:chemistry; D002352:Carrier Proteins / Q000737:chemistry; D029968:Escherichia coli Proteins; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010196:Pancreatic Elastase / Q000737:chemistry; D010206:Papain / Q000737:chemistry; D010434:Pepsin A / Q000737:chemistry; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D013820:Thermolysin / Q000737:chemistry; D013884:Thiosulfate Sulfurtransferase / Q000737:chemistry
C016242:AraF protein, E coli; D002352:Carrier Proteins; D029968:Escherichia coli Proteins; D011506:Proteins; D000426:Alcohol Dehydrogenase; D001219:Aspartate Aminotransferases; D013884:Thiosulfate Sulfurtransferase; D010196:Pancreatic Elastase; D010206:Papain; D010434:Pepsin A; D013820:Thermolysin; D000154:Aconitate Hydratase