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Prediction of protein relative solvent accessibility with support vector machines and long-range interaction 3D local descriptor †
Article first published online: 12 DEC 2003
Copyright © 2003 Wiley-Liss, Inc.
Proteins: Structure, Function, and Bioinformatics
Volume 54, Issue 3, pages 557–562, 15 February 2004
How to Cite
Kim, H. and Park, H. (2004), Prediction of protein relative solvent accessibility with support vector machines and long-range interaction 3D local descriptor . Proteins, 54: 557–562. doi: 10.1002/prot.10602
- Issue published online: 21 JAN 2004
- Article first published online: 12 DEC 2003
- Manuscript Accepted: 27 JUL 2003
- Manuscript Received: 31 JAN 2003
- National Science Foundation. Grant Numbers: CCR-0204109, ACI-0305543
- protein structure prediction;
- solvent accessibility;
- support vector machines;
- directed acyclic graph scheme;
- long range interaction
The prediction of protein relative solvent accessibility gives us helpful information for the prediction of tertiary structure of a protein. The SVMpsi method, which uses support vector machines (SVMs), and the position-specific scoring matrix (PSSM) generated from PSI-BLAST have been applied to achieve better prediction accuracy of the relative solvent accessibility. We have introduced a three-dimensional local descriptor that contains information about the expected remote contacts by both the long-range interaction matrix and neighbor sequences. Moreover, we applied feature weights to kernels in SVMs in order to consider the degree of significance that depends on the distance from the specific amino acid. Relative solvent accessibility based on a two state-model, for 25%, 16%, 5%, and 0% accessibility are predicted at 78.7%, 80.7%, 82.4%, and 87.4% accuracy, respectively. Three-state prediction results provide a 64.5% accuracy with 9%; 36% threshold. The support vector machine approach has successfully been applied for solvent accessibility prediction by considering long-range interaction and handling unbalanced data. Proteins 2004;54:000–000. © 2003 Wiley-Liss, Inc.