Review Article

A Survey of Computational Intelligence Techniques in Protein Function Prediction

Table 3

Summary of computational intelligence (CI) techniques in prediction of enzyme function/family.

Ref.CI techniquesPerformanceDatasets

[70]-NNAccuracy: 85%Functional domain composition
[71]-NNAccuracy: 76.6%Amphiphilic pseudoamino acid composition
[72]OET-NNOverall accuracy: 91.3%, 93.7%, and 98.3% for the 1st, 2nd, and 3rd levelFunctional domain composition and PSSM
[73]-NNAccuracy: 99% Amino acid composition
[74]Fuzzy -NNAccuracy: 56.9%Pseudoamino acid composition, approximate entropy, and hydrophobicity
[75] SVMAccuracy: 80.87%Amphiphilic pseudo amino acid composition
[76]SVM with DWTAccuracy: 91.9.Pseudoamino acid composition
[77]SVMMCC: 0.92 and accuracy: 93% Pseudoamino acid composition with CTF
[78]SVMAccuracy: 91.32% Functional domain composition
[79]SVMAccuracy: 81% to 98%  and MCC: 0.82 to 0.98Pseudoamino acid composition with CTF
[20]SVMAccuracy: 95.25%Structural features based on fragment libraries
[80]SVMAccuracy: 69.1–99.6%Amino acid sequence
[81]SVMSensitivity: 85.6% and specificity: 86.1%Pseudoamino acid composition
[82]SVMAccuracy: 77.4%Sequence similarity, amino acid composition, physiochemical properties, and dipeptide composition
[83]Bayesian classifierAccuracy: 45%Structural properties
[84]Random forestOverall accuracy: 94.87%, 87.7%, and 84.25% for the 1st, 2nd, and 3rd levelSequence derived features
[85]Random forestPrecision: 0.98 and recall: 0.89Set of specificity determining residues
[86]SVM and random forestAccuracy: 71.29–99.53% by SVM and 94–99.31% by random forestSequence derived properties
[87]N-to-1 neural networkOverall accuracy: 96%, specificity: 80%, and FP rates: 7%Amino acid sequences