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BMCBI
2008

Sequence based residue depth prediction using evolutionary information and predicted secondary structure

11 years 6 months ago
Sequence based residue depth prediction using evolutionary information and predicted secondary structure
Background: Residue depth allows determining how deeply a given residue is buried, in contrast to the solvent accessibility that differentiates between buried and solvent-exposed residues. When compared with the solvent accessibility, the depth allows studying deep-level structures and functional sites, and formation of the protein folding nucleus. Accurate prediction of residue depth would provide valuable information for fold recognition, prediction of functional sites, and protein design. Results: A new method, RDPred, for the real-value depth prediction from protein sequence is proposed. RDPred combines information extracted from the sequence, PSI-BLAST scoring matrices, and secondary structure predicted with PSIPRED. Threefold/ten-fold cross validation based tests performed on three independent, low-identity datasets show that the distance based depth (computed using MSMS) predicted by RDPred is characterized by 0.67/0.67, 0.66/0.67, and 0.64/0.65 correlation with the actual dept...
Hua Zhang, Tuo Zhang, Ke Chen 0003, Shiyi Shen, Ji
Added 09 Dec 2010
Updated 09 Dec 2010
Type Journal
Year 2008
Where BMCBI
Authors Hua Zhang, Tuo Zhang, Ke Chen 0003, Shiyi Shen, Jishou Ruan, Lukasz A. Kurgan
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