| Reference |
Methods (URL) |
Features |
| Chou et al. [8] |
CDA |
AAC |
| Chou [9] |
CDA |
AmPseAAC |
| Shah et al. [2] |
BLAST, FASTA |
Sequence information |
| Audit et al. [14] |
BLAST |
Sequence information |
| Tian et al. [6] |
PSI-BLAST |
Sequence and function information |
| Espadaler et al. [7] |
PSI-BLAST and BLAST |
Sequence information and protein interactions |
| Otto et al. [16] |
BLASTp and HMMer |
Sequence information |
| Galperin et al. [17] |
PSI-BLAST |
Sequence information |
| Chou et al. [10] |
Statistical analysis |
PseAAC |
| Bray et al. [25] |
Statistical analysis |
Structural and sequence properties |
| Munteanu et al. [19] |
Statistical analysis |
Structural properties and AAC |
| Cai et al. [31] |
NN |
Domain composition (GO) and PseAAC |
| Cai et al. [4] |
NN |
Domain composition (interPro) |
| EzyPred [34] |
NN( http://www.csbio.sjtu.edu.cn/bioinf/EzyPred/) |
Domain composition (Pfam) and Evolutionary information |
| Nasibov et al. [42] |
K-NN |
AAC |
| Huang et al. [41] |
AFK-NN |
AmPseAAC |
| Chou et al. [30] |
ISort |
Domain composition (GO) and AmPseAAC |
| Cai et al. [32] |
ISort |
Domain composition (interPro) and PseAAC |
| Borro et al. [53] |
Bayesian |
Structural information |
| Levy et al. [54] |
Bayesian |
Sequence information |
| Detect [55] |
Bayesian |
Sequence information |
| Latino et al. [52] |
SOM |
Physicochemical and topology descriptors |
| SVMProt [43,44] |
SVM (http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi) |
AAC |
| ECS [33] |
SVM ( http://pcal.biosino.org/enzyme_classification.html) |
Domain composition (Pfam) |
| Dobson et al. [18] |
SVM |
Structural properties |
| ASC [20] |
SVM (http://asc.informatik.uni-tuebingen.de) |
Structural and sequence properties |
| SPSearch [38] |
SVM ( http://adios.tau.ac.il/SPSearch/) |
Specific peptides ( MEX[38]) |
| Qiu et al. [46] |
SVM |
PseAAC |
| Wang et al. [48] |
SVM |
AAC and Neighbor relationships |
| Shi et al. [47] |
SVM |
PseAAC |
| Almonacid et al. [28] |
Tanimoto coefficients and similarity search |
Structural information |
| Almonacid et al. [29] |
Tanimoto coefficients and similarity search |
Structural information |
| Kristensen et al. [27] |
Structure template matching |
Structural information (Evolutionary) |
| Kato et al. [23] |
Structure template matching |
Structural properties |
| Concu et al. [21] |
LDA and ANN |
Structural information |
| Concu et al. [22] |
LDA and ANN (http://miaja.tic.udc.es/Bio-AIMS/EnzClassPred.php) |
Structural information |
| Astikainen et al. [49] |
HM3 algorithm |
String kernels |
| DME [39] |
MEX [38] ( http://adios.tau.ac.il/DME/) |
Specific peptides ( MEX[38]) |
| Liewlom et al. [40] |
Mutation control |
Reactive motifs |
| Izrailev et al. [24] |
Nearest neighbor distance |
Ligand interactions |
| EFICAz [60] |
Ensemble |
Sequence similarity, Pfam and Prosite patterns |
| EFICAz2 [61] |
Ensemble (http:/cssb.biology.gatech.edu/skolnick/webservice/EFICAz2/index.html) |
Sequence similarity, Pfam and Prosite patterns |
| Umar et al. [62] |
Ensemble |
Sequence and structure information |
| Kumar et al. [63] |
Ensemble |
Sequence information |
| Wang et al. [65] |
Ensemble |
AAC and Neighbor relationships |
