Abstract
Prediction of protein residue contact is one of the important two-dimensional prediction tasks in protein structure prediction. The residue contact map of protein contains information which represents three-dimensional conformation of protein. However the accuracy of the prediction is dependent on the type of protein information used to distinguish between contacts or non-contacts. According to CASP (Critical Assessment of Techniques of Protein Structure Prediction) the accuracy of protein contact map prediction is still low due to the behaviour of the predictors developed where the predictors only effective against specific type of protein structure. In order to further improve the performance of the predictor, effective features must be identified and used. Therefore, this research is conducted to determine the effectiveness of the existing features used in protein contact map prediction.
Keywords
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Cheng, J., Baldi, P.: Improved Residue Contact Prediction Using Support Vector Machines and A Large Feature Set. BMC Bioinformatics 8, 113 (2007)
Yuan, X., Bystroff, C.: Protein Contact Map Prediction. In: Xu, Y., Xu, D., Liang, J. (eds.) Computational Methods for Protein Structure Prediction and Modeling, pp. 255–277. Springer, Heidelberg (2007)
Bartoli, L., Capriotti, E., Fariselli, P., Martelli, P.L., Casadio, R.: The Pros and Cons of Predicting Protein Contact Maps. In: Zaki, M., Bystroff, C. (eds.) Protein Structure Prediction Second Edition, pp. 199–217. Humana Press, Totawa (2008)
Cheng, J., Randall, A., Sweredoski, M., Baldi, P.: SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Research 72–76 (2005)
Huang, E., Subbiah, S., Tsai, J., Levitt, M.: Using a Hydrophobic Contact Potential to Evaluate Native and Near-Native Folds Generated by Molecular Dynamics Simulations. J. Mol. Biol. 257, 716–725 (1996)
Miyazawa, S., Jernigan, R.: An empirical energy potential with a reference state for protein fold and sequence recognition. Proteins 36, 357–369 (1999)
Zhu, H., Braun, W.: Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting. Protein Sci. 8, 326–342 (1999)
MacCallum: Striped Sheets and Protein Contact Prediction. Oxford Bioinformatics 20, 224–231 (2004)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Chan, W.H., Mohamad, M.S. (2012). Prediction of Protein Residue Contact Using Support Vector Machine. In: Lukose, D., Ahmad, A.R., Suliman, A. (eds) Knowledge Technology. KTW 2011. Communications in Computer and Information Science, vol 295. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-32826-8_33
Download citation
DOI: https://doi.org/10.1007/978-3-642-32826-8_33
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-32825-1
Online ISBN: 978-3-642-32826-8
eBook Packages: Computer ScienceComputer Science (R0)