Prediction of protein solvent accessibility using fuzzy k-nearest neighbor method.
BACKGROUND
The solvent accessibility of amino acid residues plays an important role in tertiary structure prediction, especially in the absence of significant sequence similarity of a query protein to those with known structures. The prediction of solvent accessibility is less accurate than secondary structure prediction in spite of improvements in recent researches. The k-nearest neighbor method, a simple but powerful classification algorithm, has never been applied to the prediction of solvent accessibility, although it has been used frequently for the classification of biological and medical data.


RESULTS
We applied the fuzzy k-nearest neighbor method to the solvent accessibility prediction, using PSI-BLAST profiles as feature vectors, and achieved high prediction accuracies. With leave-one-out cross-validation on the ASTRAL SCOP reference dataset constructed by sequence clustering, our method achieved 64.1% accuracy for a 3-state (buried/intermediate/exposed) prediction (thresholds of 9% for buried/intermediate and 36% for intermediate/exposed) and 86.7, 82.0, 79.0 and 78.5% accuracies for 2-state (buried/exposed) predictions (thresholds of each 0, 5, 16 and 25% for buried/exposed), respectively. Our method also showed slightly better accuracies than other methods by about 2-5% on the RS126 dataset and a benchmarking dataset with 229 proteins.


BACKGROUND
Program and datasets are available at http://biocom1.ssu.ac.kr/FKNNacc/


BACKGROUND
jul@ssu.ac.kr.
Sim
Jaehyun
J
Department of Bioinformatics and Life Science, Bioinformatics and Molecular Design Technology Innovation Center, Soongsil University, Seoul 156-743, South Korea.
Kim
Seung-Yeon
SY
Lee
Julian
J
D000465:Algorithms; D016000:Cluster Analysis; D003198:Computer Simulation; D017143:Fuzzy Logic; D008956:Models, Chemical; D008958:Models, Molecular; D009716:Numerical Analysis, Computer-Assisted; D010363:Pattern Recognition, Automated / Q000379:methods; D011487:Protein Conformation; D011506:Proteins / Q000032:analysis / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012997:Solvents / Q000737:chemistry*
D011506:Proteins; D012997:Solvents