Real value prediction of protein solvent accessibility using enhanced PSSM features.
BACKGROUND
Prediction of protein solvent accessibility, also called accessible surface area (ASA) prediction, is an important step for tertiary structure prediction directly from one-dimensional sequences. Traditionally, predicting solvent accessibility is regarded as either a two- (exposed or buried) or three-state (exposed, intermediate or buried) classification problem. However, the states of solvent accessibility are not well-defined in real protein structures. Thus, a number of methods have been developed to directly predict the real value ASA based on evolutionary information such as position specific scoring matrix (PSSM).


RESULTS
This study enhances the PSSM-based features for real value ASA prediction by considering the physicochemical properties and solvent propensities of amino acid types. We propose a systematic method for identifying residue groups with respect to protein solvent accessibility. The amino acid columns in the PSSM profile that belong to a certain residue group are merged to generate novel features. Finally, support vector regression (SVR) is adopted to construct a real value ASA predictor. Experimental results demonstrate that the features produced by the proposed selection process are informative for ASA prediction.


CONCLUSIONS
Experimental results based on a widely used benchmark reveal that the proposed method performs best among several of existing packages for performing ASA prediction. Furthermore, the feature selection mechanism incorporated in this study can be applied to other regression problems using the PSSM. The program and data are available from the authors upon request.
Chang
Darby Tien-Hao
DT
Department of Electrical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan, R.O.C. darby@ee.ncku.edu.tw
Huang
Hsuan-Yu
HY
Syu
Yu-Tang
YT
Wu
Chih-Peng
CP
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D002627:Chemistry, Physical / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D015233:Models, Statistical; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012044:Regression Analysis; D015203:Reproducibility of Results; D020539:Sequence Analysis, Protein; D012984:Software; D012997:Solvents / Q000737:chemistry*; D013499:Surface Properties
D000596:Amino Acids; D011506:Proteins; D012997:Solvents