title: RSARF: prediction of residue solvent accessibility from protein sequence using random forest method.
abstract: Prediction of protein structure from its amino acid sequence is still a challenging problem. The complete physicochemical understanding of protein folding is essential for the accurate structure prediction. Knowledge of residue solvent accessibility gives useful insights into protein structure prediction and function prediction. In this work, we propose a random forest method, RSARF, to predict residue accessible surface area from protein sequence information. The training and testing was performed using 120 proteins containing 22006 residues. For each residue, buried and exposed state was computed using five thresholds (0%, 5%, 10%, 25%, and 50%). The prediction accuracy for 0%, 5%, 10%, 25%, and 50% thresholds are 72.9%, 78.25%, 78.12%, 77.57% and 72.07% respectively. Further, comparison of RSARF with other methods using a benchmark dataset containing 20 proteins shows that our approach is useful for prediction of residue solvent accessibility from protein sequence without using structural information. The RSARF program, datasets and supplementary data are available at http://caps.ncbs.res.in/download/pugal/RSARF/.
authors.affiliation: Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore. gpugal@gmail.com
authors.forename: Ganesan
authors.initials: G
authors.lastname: Pugalenthi
authors.forename: Krishna Kumar
authors.initials: KK
authors.lastname: Kandaswamy
authors.forename: Kuo-Chen
authors.initials: KC
authors.lastname: Chou
authors.forename: Saravanan
authors.initials: S
authors.lastname: Vivekanandan
authors.forename: Prasanna
authors.initials: P
authors.lastname: Kolatkar
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D057927:Hydrophobic and Hydrophilic Interactions; D008969:Molecular Sequence Data; D011237:Predictive Value of Tests; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D012997:Solvents / Q000737:chemistry
chemical_list: D011506:Proteins; D012997:Solvents