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Bioinformatics Vol. 19 no. 14 2003
Pages 1849-1851
© 2003 Oxford University Press

Applications Note

RVP-net: online prediction of real valued accessible surface area of proteins from single sequences

Shandar Ahmad 1,*, M. Michael Gromiha 2 and Akinori Sarai 1

1 Department of Biochemical Engineering and Science, Kyushu Institute of Technology, IZUKA, 820 8502, Fukuoka-ken, Japan and 2 Computational Biology Research Center (CBRC), AIST, 2-41-6, Koto-ku, Tokyo 135 0064, Japan

Received on December 19, 2002 ; revised on March 11, 2003 ; accepted on April 7, 2003

Summary: RVP-net is an online program for the prediction of real valued solvent accessibility. All previous methods of accessible surface area (ASA) predictions classify amino acid residues into exposure states and named them buried or exposed based on different thresholds. Real values in some cases were generated by taking the mid points of these state thresholds. This is the first method, which provides a direct prediction of ASA without making exposure categories and achieves results better than 19% mean absolute error. To facilitate batch processing of several sequences, a standalone version of this tool is also provided.

Availability: Online predictions are available at http://www.netasa.org/rvp-net/. Standalone version of the program can be obtained from the corresponding author by E-mail request.

Contact: shandar{at}bse.kyutech.ac.jp

* To whom correspondence should be addressed.


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