论文信息 - Prediction of FAD Binding Residues with Combined Features from Primary Sequence

Prediction of FAD Binding Residues with Combined Features from Primary Sequence

In order to analyze the impact of different characteristics of protein sequence on small nucleotide binding site prediction, this paper proposed four sequence-based methods for identifying FAD binding residues of flavin binding proteins (FBP) by means of support vector machine (SVM). We used the different combined features obtained from primary sequence as input for the prediction: evolutionary conservation, predicated solvent accessibility, physicochemical characteristics, residue neighbor list and so on. Our result shows that, the three methods which combined the evolutionary information performed much better than the predictor which did not adopt the evolutionary information. The predictor which combined the feature of residue neighbor list, evolutionary information and physicochemical properties performs the best, achieved accuracy of 87.7326% which is 4.87% higher than the previous methods.

H. Yamana | Chun Fang | T. Noguchi

[1] O. Dym,et al. Sequence‐structure analysis of FAD‐containing proteins , 2001, Protein science : a publication of the Protein Society.

[2] V. Sobolev,et al. Conserved positions for ribose recognition: importance of water bridging interactions among ATP, ADP and FAD-protein complexes. , 2002, Journal of molecular biology.

[3] M. Gromiha,et al. Real value prediction of solvent accessibility from amino acid sequence , 2003, Proteins.

[4] Baldomero Oliva,et al. Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships , 2005, Bioinform..

[5] M. Go,et al. An empirical approach for detecting nucleotide-binding sites on proteins. , 2006, Protein engineering, design & selection : PEDS.

[6] Burkhard Rost,et al. Prediction of DNA-binding residues from sequence , 2007, ISMB/ECCB.

[7] Gajendra P.S. Raghava,et al. Prediction of RNA binding sites in a protein using SVM and PSSM profile , 2008, Proteins.

[8] Ozlem Keskin,et al. A survey of available tools and web servers for analysis of protein-protein interactions and interfaces , 2008, Briefings Bioinform..

[9] Xue-wen Chen,et al. Sequence-based prediction of protein interaction sites with an integrative method , 2009, Bioinform..

[10] Gajendra P. S. Raghava,et al. Prediction of FAD interacting residues in a protein from its primary sequence using evolutionary information , 2010, BMC Bioinformatics.