Prediction of gamma-turns from amino acid sequences.
We predicted gamma-turns from amino acid sequences using the first-order Markov chain theory and enlarged representative data sets corresponding to protein chains selected from the Protein Data Bank (PDB). The following data sets were used for training and deriving the probability values: (1) an initial data set containing 315 protein chains comprising 904 gamma-turns and (2) a later data set in order to include new entries in the PDB, containing 434 protein chains and comprising 1053 gamma-turns. By excluding 93 protein chains that were common to these two training data sets, we generated two mutually exclusive data sets containing 222 and 341 protein chains for testing our predictions. Applying amino acid probability values derived from training data sets on to testing data sets yielded overall prediction accuracies in the range 54-57%. We recommend the use of probability values derived from the data set comprising 315 protein chains that represents more gamma-turns and also provides better predictions.
Guruprasad
K
K
Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad - 500 007, India. guru@ccmb.res.in
Shukla
S
S
Adindla
S
S
Guruprasad
L
L
D000595:Amino Acid Sequence; D008390:Markov Chains; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
D011506:Proteins