Protein Engineering vol. 16 no. 12 pp. 987-992, 2003
© 2003 Oxford University Press
Improvement in prediction of solvent accessibility by probability profiles
1Dipartimento di Scienze Biochimiche ‘A. Rossi Fanelli’ and Istituto di Biologia e Patologia Molecolare del C.N.R., 2Centro di Eccellenza di Biologia e Medicina Molecolare (BEMM), Università ‘La Sapienza’, 00185 Rome and 4Centro Interdipartimentale di Ricerca per l’Analisi dei Modelli e dell’Informazione nei Sistemi Biomedici (CISB), Italy
3 To whom correspondence should be addressed at: Dipartimento di Scienze Biochimiche, Università ‘La Sapienza’, P.le A. Moro, 5, 00185 Roma, Italy. e-mail: giulio.gianese{at}uniroma1.it
The capability of predicting folding and conformation of a protein from its primary structure is probably one of the main goals of modern biology. An accurate prediction of solvent accessibility is an intermediate step along this way. A new method for predicting solvent accessibility from single sequence and multiple alignment data is described. The method is based on probability profiles calculated on an amino acid sequence centred on the residue whose accessibility has to be predicted. A profile is constructed for each exposure category considered so as to calculate the probability of a sequence being generated by the different profiles. Prediction accuracy was tested on a variety of protein sets with two- and three-state models. Different thresholds were used according to those adopted by the authors proposing the data sets. The prediction accuracy is significantly improved over existing methods.
Received June 23, 2003; revised October 25, 2003; accepted October 30, 2003
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