A High Performing Tool for Residue Solvent Accessibility Prediction

  • Lorenzo Palmieri
  • Maria Federico
  • Mauro Leoncini
  • Manuela Montangero
Conference paper

DOI: 10.1007/978-3-642-23208-4_13

Part of the Lecture Notes in Computer Science book series (LNCS, volume 6865)
Cite this paper as:
Palmieri L., Federico M., Leoncini M., Montangero M. (2011) A High Performing Tool for Residue Solvent Accessibility Prediction. In: Böhm C., Khuri S., Lhotská L., Pisanti N. (eds) Information Technology in Bio- and Medical Informatics. ITBAM 2011. Lecture Notes in Computer Science, vol 6865. Springer, Berlin, Heidelberg

Abstract

Many efforts were spent in the last years in bridging the gap between the huge number of sequenced proteins and the relatively few solved structures. Relative Solvent Accessibility (RSA) prediction of residues in protein complexes is a key step towards secondary structure and protein-protein interaction sites prediction. With very different approaches, a number of software tools for RSA prediction have been produced throughout the last twenty years. Here, we present a binary classifier which implements a new method mainly based on sequence homology and implemented by means of look-up tables. The tool exploits residue similarity in solvent exposure pattern of neighboring context in similar protein chains, using BLAST search and DSSP structure. A two-state classification with 89.5% accuracy and 0.79 correlation coefficient against the real data is achieved on a widely used dataset.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Lorenzo Palmieri
    • 1
  • Maria Federico
    • 1
  • Mauro Leoncini
    • 1
    • 2
  • Manuela Montangero
    • 1
    • 2
  1. 1.Dipartimento di Ingegneria dell’InformazioneUniversità di Modena e Reggio EmiliaItaly
  2. 2.CNRIstituto di Informatica e TelematicaPisaItaly

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