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<datestamp>2017-12-21</datestamp>
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<publisher>HAL CCSD</publisher>
<title lang=en>A new prediction strategy for long local protein structures using an original description.</title>
<title lang=ro> : Protein Long Local Structure Prediction</title>
<creator>Bornot, Aurélie</creator>
<creator>Etchebest, Catherine</creator>
<creator>De Brevern, Alexandre</creator>
<contributor>Bioinformatique génomique et moléculaire ; Université Paris Diderot - Paris 7 (UPD7) - Institut National de la Santé et de la Recherche Médicale (INSERM)</contributor>
<contributor>Institut National de la Transfusion Sanguine [Paris] (INTS)</contributor>
<contributor>Protéines de la membrane érythrocytaire et homologues non-érythroides ; Université des Antilles et de la Guyane (UAG) - Institut National de la Transfusion Sanguine [Paris] (INTS) - Université Paris Diderot - Paris 7 (UPD7) - Université de la Réunion (UR) - Institut National de la Santé et de la Recherche Médicale (INSERM)</contributor>
<description>International audience</description>
<source>ISSN: 0887-3585</source>
<source>EISSN: 1097-0134</source>
<source>Proteins - Structure, Function and Bioinformatics</source>
<publisher>Wiley</publisher>
<identifier>inserm-00348740</identifier>
<identifier>http://www.hal.inserm.fr/inserm-00348740</identifier>
<identifier>http://www.hal.inserm.fr/inserm-00348740/document</identifier>
<identifier>http://www.hal.inserm.fr/inserm-00348740/file/Bornot_Proteins_2009_preprint_version.pdf</identifier>
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<source>http://www.hal.inserm.fr/inserm-00348740</source>
<source>Proteins - Structure, Function and Bioinformatics, Wiley, 2009, 76 (3), pp.570-87. 〈10.1002/prot.22370〉</source>
<identifier>DOI : 10.1002/prot.22370</identifier>
<relation>info:eu-repo/semantics/altIdentifier/doi/10.1002/prot.22370</relation>
<identifier>PUBMED : 19241475</identifier>
<relation>info:eu-repo/semantics/altIdentifier/pmid/19241475</relation>
<language>en</language>
<subject lang=en>ab initio</subject>
<subject lang=en>library of fragments</subject>
<subject lang=en>structural networks</subject>
<subject lang=en>local structure prediction</subject>
<subject lang=en>support vector machines</subject>
<subject lang=en>ab initio.</subject>
<subject>[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology</subject>
<subject>[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]</subject>
<subject>[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]</subject>
<subject>[SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN]</subject>
<type>info:eu-repo/semantics/article</type>
<type>Journal articles</type>
<description lang=en>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.</description>
<date>2009-01-14</date>
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