Skip to Main content Skip to Navigation
Journal articles

A structural alphabet for local protein structures: improved prediction methods.

Abstract : Three-dimensional protein structures can be described with a library of 3D fragments that define a structural alphabet. We have previously proposed such an alphabet, composed of 16 patterns of five consecutive amino acids, called Protein Blocks (PBs). These PBs have been used to describe protein backbones and to predict local structures from protein sequences. The Q16 prediction rate reaches 40.7% with an optimization procedure. This article examines two aspects of PBs. First, we determine the effect of the enlargement of databanks on their definition. The results show that the geometrical features of the different PBs are preserved (local RMSD value equal to 0.41 A on average) and sequence-structure specificities reinforced when databanks are enlarged. Second, we improve the methods for optimizing PB predictions from sequences, revisiting the optimization procedure and exploring different local prediction strategies. Use of a statistical optimization procedure for the sequence-local structure relation improves prediction accuracy by 8% (Q16 = 48.7%). Better recognition of repetitive structures occurs without losing the prediction efficiency of the other local folds. Adding secondary structure prediction improved the accuracy of Q16 by only 1%. An entropy index (Neq), strongly related to the RMSD value of the difference between predicted PBs and true local structures, is proposed to estimate prediction quality. The Neq is linearly correlated with the Q16 prediction rate distributions, computed for a large set of proteins. An "expected" prediction rate QE16 is deduced with a mean error of 5%.
Complete list of metadata
Contributor : Alexandre G. de Brevern Connect in order to contact the contributor
Submitted on : Thursday, April 26, 2007 - 9:24:20 AM
Last modification on : Saturday, June 25, 2022 - 8:46:44 PM
Long-term archiving on: : Friday, November 25, 2016 - 3:30:05 PM


 Restricted access
To satisfy the distribution rights of the publisher, the document is embargoed until : jamais

Please log in to resquest access to the document




Catherine Etchebest, Cristina Benros, Serge A. Hazout, Alexandre de Brevern. A structural alphabet for local protein structures: improved prediction methods.. Proteins - Structure, Function and Bioinformatics, Wiley, 2005, 59 (4), pp.810-27. ⟨10.1002/prot.20458⟩. ⟨inserm-00143564⟩



Record views