A new prediction strategy for long local protein structures using an original description. - Inserm - Institut national de la santé et de la recherche médicale Accéder directement au contenu
Article Dans Une Revue Proteins - Structure, Function and Bioinformatics Année : 2009

A new prediction strategy for long local protein structures using an original description.

Résumé

A relevant and accurate description of three-dimensional (3D) protein structures can be achieved by characterizing recurrent local structures. In a previous study, we developed a library of 120 3D structural prototypes encompassing all known 11-residues long local protein structures and ensuring a good quality of structural approximation. A local structure prediction method was also proposed. Here, overlapping properties of local protein structures in global ones are taken into account to characterize frequent local networks. At the same time, we propose a new long local structure prediction strategy which involves the use of evolutionary information coupled with Support Vector Machines (SVMs). Our prediction is evaluated by a stringent geometrical assessment. Every local structure prediction with a Calpha RMSD less than 2.5 A from the true local structure is considered as correct. A global prediction rate of 63.1% is then reached, corresponding to an improvement of 7.7 points compared with the previous strategy. In the same way, the prediction of 88.33% of the 120 structural classes is improved with 8.65% mean gain. 85.33% of proteins have better prediction results with a 9.43% average gain. An analysis of prediction rate per local network also supports the global improvement and gives insights into the potential of our method for predicting super local structures. Moreover, a confidence index for the direct estimation of prediction quality is proposed. Finally, our method is proved to be very competitive with cutting-edge strategies encompassing three categories of local structure predictions. Proteins 2009. (c) 2009 Wiley-Liss, Inc.
Fichier principal
Vignette du fichier
Bornot_Proteins_2009_preprint_version.pdf (3.11 Mo) Télécharger le fichier
Supplementary_material_for_review_1.doc (30.5 Ko) Télécharger le fichier
Supplementary_material_for_review_2.doc (166.5 Ko) Télécharger le fichier
Supplementary_material_for_review_3.doc (444 Ko) Télécharger le fichier
Supplementary_material_for_review_4.doc (399 Ko) Télécharger le fichier
Supplementary_material_for_review_5.doc (267 Ko) Télécharger le fichier
Supplementary_material_for_review_6.doc (281 Ko) Télécharger le fichier
Supplementary_material_for_review_7.doc (286.5 Ko) Télécharger le fichier
Supplementary_material_for_review_8.doc (29.5 Ko) Télécharger le fichier
inserm-00348740_edited.pdf (1.4 Mo) Télécharger le fichier
Origine : Fichiers produits par l'(les) auteur(s)
Format : Autre
Format : Autre
Format : Autre
Format : Autre
Format : Autre
Format : Autre
Format : Autre
Format : Autre
Origine : Fichiers produits par l'(les) auteur(s)
Loading...

Dates et versions

inserm-00348740 , version 1 (04-09-2009)

Identifiants

Citer

Aurélie Bornot, Catherine Etchebest, Alexandre de Brevern. A new prediction strategy for long local protein structures using an original description.. Proteins - Structure, Function and Bioinformatics, 2009, 76 (3), pp.570-87. ⟨10.1002/prot.22370⟩. ⟨inserm-00348740⟩
233 Consultations
562 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More