Curation
Accueil
Racine
Curation
Exploration
Accueil
Racine
Accueil
Racine

Serveur d'exploration MERS

Attention, ce site est en cours de développement !
Attention, site généré par des moyens informatiques à partir de corpus bruts.
Les informations ne sont donc pas validées.

Reduced Fragment Diversity for Alpha and Alpha-Beta Protein Structure Prediction using Rosetta.

Identifieur interne : 000C11 ( Main/Curation ); précédent : 000C10; suivant : 000C12

Reduced Fragment Diversity for Alpha and Alpha-Beta Protein Structure Prediction using Rosetta.

Auteurs : Jad Abbass [Royaume-Uni] ; Jean-Christophe Nebel

Source :

RBID : pubmed:27993124

Descripteurs français

English descriptors

Abstract

Protein structure prediction is considered a main challenge in computational biology. The biannual international competition, Critical Assessment of protein Structure Prediction (CASP), has shown in its eleventh experiment that free modelling target predictions are still beyond reliable accuracy, therefore, much effort should be made to improve ab initio methods. Arguably, Rosetta is considered as the most competitive method when it comes to targets with no homologues. Relying on fragments of length 9 and 3 from known structures, Rosetta creates putative structures by assembling candidate fragments. Generally, the structure with the lowest energy score, also known as first model, is chosen to be the "predicted one". A thorough study has been conducted on the role and diversity of 3-mers involved in Rosetta's model "refinement" phase. Usage of the standard number of 3-mers - i.e. 200 - has been shown to degrade alpha and alpha-beta protein conformations initially achieved by assembling 9-mers. Therefore, a new prediction pipeline is proposed for Rosetta where the "refinement" phase is customised according to a target's structural class prediction. Over 8% improvement in terms of first model structure accuracy is reported for alpha and alpha-beta classes when decreasing the number of 3- mers.

DOI: 10.2174/0929866523666161216124019
PubMed: 27993124

Links toward previous steps (curation, corpus...)

Links to Exploration step

pubmed:27993124

Le document en format XML

<record>
<TEI>
<teiHeader>
<fileDesc>
<titleStmt>
<title xml:lang="en">Reduced Fragment Diversity for Alpha and Alpha-Beta Protein Structure Prediction using Rosetta.</title>
<author>
<name sortKey="Abbass, Jad" sort="Abbass, Jad" uniqKey="Abbass J" first="Jad" last="Abbass">Jad Abbass</name>
<affiliation wicri:level="1">
<nlm:affiliation>Faculty of Science, Engineering and Computing, Kingston; University, London, KT1 2EE, United Kingdom.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Faculty of Science, Engineering and Computing, Kingston; University, London, KT1 2EE</wicri:regionArea>
<wicri:noRegion>KT1 2EE</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Nebel, Jean Christophe" sort="Nebel, Jean Christophe" uniqKey="Nebel J" first="Jean-Christophe" last="Nebel">Jean-Christophe Nebel</name>
</author>
</titleStmt>
<publicationStmt>
<idno type="wicri:source">PubMed</idno>
<date when="2017">2017</date>
<idno type="RBID">pubmed:27993124</idno>
<idno type="pmid">27993124</idno>
<idno type="doi">10.2174/0929866523666161216124019</idno>
<idno type="wicri:Area/PubMed/Corpus">000E46</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000E46</idno>
<idno type="wicri:Area/PubMed/Curation">000E46</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000E46</idno>
<idno type="wicri:Area/PubMed/Checkpoint">000B50</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000B50</idno>
<idno type="wicri:Area/Ncbi/Merge">001888</idno>
<idno type="wicri:Area/Ncbi/Curation">001888</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">001888</idno>
<idno type="wicri:Area/Main/Merge">000C14</idno>
<idno type="wicri:Area/Main/Curation">000C11</idno>
</publicationStmt>
<sourceDesc>
<biblStruct>
<analytic>
<title xml:lang="en">Reduced Fragment Diversity for Alpha and Alpha-Beta Protein Structure Prediction using Rosetta.</title>
<author>
<name sortKey="Abbass, Jad" sort="Abbass, Jad" uniqKey="Abbass J" first="Jad" last="Abbass">Jad Abbass</name>
<affiliation wicri:level="1">
<nlm:affiliation>Faculty of Science, Engineering and Computing, Kingston; University, London, KT1 2EE, United Kingdom.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Faculty of Science, Engineering and Computing, Kingston; University, London, KT1 2EE</wicri:regionArea>
<wicri:noRegion>KT1 2EE</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Nebel, Jean Christophe" sort="Nebel, Jean Christophe" uniqKey="Nebel J" first="Jean-Christophe" last="Nebel">Jean-Christophe Nebel</name>
</author>
</analytic>
<series>
<title level="j">Protein and peptide letters</title>
<idno type="eISSN">1875-5305</idno>
<imprint>
<date when="2017" type="published">2017</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc>
<textClass>
<keywords scheme="KwdEn" xml:lang="en">
<term>Algorithms</term>
<term>Benchmarking</term>
<term>Computational Biology (methods)</term>
<term>Computer Simulation</term>
<term>Models, Molecular</term>
<term>Peptide Fragments (chemistry)</term>
<term>Protein Conformation, alpha-Helical</term>
<term>Protein Conformation, beta-Strand</term>
<term>Protein Folding</term>
<term>Protein Interaction Domains and Motifs</term>
<term>Proteins (chemistry)</term>
<term>Software</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr">
<term>Algorithmes</term>
<term>Biologie informatique ()</term>
<term>Fragments peptidiques ()</term>
<term>Logiciel</term>
<term>Modèles moléculaires</term>
<term>Motifs et domaines d'intéraction protéique</term>
<term>Pliage des protéines</term>
<term>Protéines ()</term>
<term>Référenciation</term>
<term>Simulation numérique</term>
<term>Structure en brin bêta</term>
<term>Structure en hélice alpha</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en">
<term>Peptide Fragments</term>
<term>Proteins</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en">
<term>Computational Biology</term>
</keywords>
<keywords scheme="MESH" xml:lang="en">
<term>Algorithms</term>
<term>Benchmarking</term>
<term>Computer Simulation</term>
<term>Models, Molecular</term>
<term>Protein Conformation, alpha-Helical</term>
<term>Protein Conformation, beta-Strand</term>
<term>Protein Folding</term>
<term>Protein Interaction Domains and Motifs</term>
<term>Software</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr">
<term>Algorithmes</term>
<term>Biologie informatique</term>
<term>Fragments peptidiques</term>
<term>Logiciel</term>
<term>Modèles moléculaires</term>
<term>Motifs et domaines d'intéraction protéique</term>
<term>Pliage des protéines</term>
<term>Protéines</term>
<term>Référenciation</term>
<term>Simulation numérique</term>
<term>Structure en brin bêta</term>
<term>Structure en hélice alpha</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front>
<div type="abstract" xml:lang="en">Protein structure prediction is considered a main challenge in computational biology. The biannual international competition, Critical Assessment of protein Structure Prediction (CASP), has shown in its eleventh experiment that free modelling target predictions are still beyond reliable accuracy, therefore, much effort should be made to improve ab initio methods. Arguably, Rosetta is considered as the most competitive method when it comes to targets with no homologues. Relying on fragments of length 9 and 3 from known structures, Rosetta creates putative structures by assembling candidate fragments. Generally, the structure with the lowest energy score, also known as first model, is chosen to be the "predicted one". A thorough study has been conducted on the role and diversity of 3-mers involved in Rosetta's model "refinement" phase. Usage of the standard number of 3-mers - i.e. 200 - has been shown to degrade alpha and alpha-beta protein conformations initially achieved by assembling 9-mers. Therefore, a new prediction pipeline is proposed for Rosetta where the "refinement" phase is customised according to a target's structural class prediction. Over 8% improvement in terms of first model structure accuracy is reported for alpha and alpha-beta classes when decreasing the number of 3- mers.</div>
</front>
</TEI>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Curation

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000C11 | SxmlIndent | more

Ou

HfdSelect -h $EXPLOR_AREA/Data/Main/Curation/biblio.hfd -nk 000C11 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Sante
   |area=    MersV1
   |flux=    Main
   |étape=   Curation
   |type=    RBID
   |clé=     pubmed:27993124
   |texte=   Reduced Fragment Diversity for Alpha and Alpha-Beta Protein Structure Prediction using Rosetta.
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Curation/RBID.i   -Sk "pubmed:27993124" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Curation/biblio.hfd   \
       | NlmPubMed2Wicri -a MersV1
Wicri

This area was generated with Dilib version V0.6.33.
Data generation: Mon Apr 20 23:26:43 2020. Site generation: Sat Mar 27 09:06:09 2021