TelematiV1, PubMed, Curation, bibRecord, 000292

Ab initio detection of fuzzy amino acid tandem repeats in protein sequences.

Identifieur interne : 000292 ( PubMed/Curation ); précédent : 000291; suivant : 000293

Ab initio detection of fuzzy amino acid tandem repeats in protein sequences.

Auteurs : Marco Pellegrini [Italie] ; Maria Elena Renda ; Alessio Vecchio

Source :

BMC bioinformatics [ 1471-2105 ] ; 2012.

RBID : pubmed:22536906

Descripteurs français

KwdFr :
- Algorithmes, Bases de données de protéines, Humains, Protéines (), Protéines (génétique), Protéines membranaires (), Protéines membranaires (génétique), Structure secondaire des protéines, Séquence d'acides aminés.
MESH :
- génétique : Protéines, Protéines membranaires.
- Algorithmes, Bases de données de protéines, Humains, Protéines, Protéines membranaires, Structure secondaire des protéines, Séquence d'acides aminés.

English descriptors

KwdEn :
- Algorithms, Amino Acid Sequence, Databases, Protein, Humans, Membrane Proteins (chemistry), Membrane Proteins (genetics), Protein Structure, Secondary, Proteins (chemistry), Proteins (genetics).
MESH :
- chemical , chemistry : Membrane Proteins, Proteins.
- chemical , genetics : Membrane Proteins, Proteins.
- Algorithms, Amino Acid Sequence, Databases, Protein, Humans, Protein Structure, Secondary.

Abstract

Tandem repetitions within protein amino acid sequences often correspond to regular secondary structures and form multi-repeat 3D assemblies of varied size and function. Developing internal repetitions is one of the evolutionary mechanisms that proteins employ to adapt their structure and function under evolutionary pressure. While there is keen interest in understanding such phenomena, detection of repeating structures based only on sequence analysis is considered an arduous task, since structure and function is often preserved even under considerable sequence divergence (fuzzy tandem repeats).

DOI: 10.1186/1471-2105-13-S3-S8
PubMed: 22536906

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Le document en format XML

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<author><name sortKey="Pellegrini, Marco" sort="Pellegrini, Marco" uniqKey="Pellegrini M" first="Marco" last="Pellegrini">Marco Pellegrini</name>
<affiliation wicri:level="1"><nlm:affiliation>Istituto di Informatica e Telematica, CNR - Consiglio Nazionale delle Ricerche, Pisa I-56124, Italy. marco.pellegrini@iit.cnr.it</nlm:affiliation>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Istituto di Informatica e Telematica, CNR - Consiglio Nazionale delle Ricerche, Pisa I-56124</wicri:regionArea>
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<author><name sortKey="Renda, Maria Elena" sort="Renda, Maria Elena" uniqKey="Renda M" first="Maria Elena" last="Renda">Maria Elena Renda</name>
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<author><name sortKey="Vecchio, Alessio" sort="Vecchio, Alessio" uniqKey="Vecchio A" first="Alessio" last="Vecchio">Alessio Vecchio</name>
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<series><title level="j">BMC bioinformatics</title>
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<term>Amino Acid Sequence</term>
<term>Databases, Protein</term>
<term>Humans</term>
<term>Membrane Proteins (chemistry)</term>
<term>Membrane Proteins (genetics)</term>
<term>Protein Structure, Secondary</term>
<term>Proteins (chemistry)</term>
<term>Proteins (genetics)</term>
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<term>Bases de données de protéines</term>
<term>Humains</term>
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<term>Protéines (génétique)</term>
<term>Protéines membranaires ()</term>
<term>Protéines membranaires (génétique)</term>
<term>Structure secondaire des protéines</term>
<term>Séquence d'acides aminés</term>
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<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Membrane Proteins</term>
<term>Proteins</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Membrane Proteins</term>
<term>Proteins</term>
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<term>Protéines membranaires</term>
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<term>Amino Acid Sequence</term>
<term>Databases, Protein</term>
<term>Humans</term>
<term>Protein Structure, Secondary</term>
</keywords>
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<term>Bases de données de protéines</term>
<term>Humains</term>
<term>Protéines</term>
<term>Protéines membranaires</term>
<term>Structure secondaire des protéines</term>
<term>Séquence d'acides aminés</term>
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<front><div type="abstract" xml:lang="en">Tandem repetitions within protein amino acid sequences often correspond to regular secondary structures and form multi-repeat 3D assemblies of varied size and function. Developing internal repetitions is one of the evolutionary mechanisms that proteins employ to adapt their structure and function under evolutionary pressure. While there is keen interest in understanding such phenomena, detection of repeating structures based only on sequence analysis is considered an arduous task, since structure and function is often preserved even under considerable sequence divergence (fuzzy tandem repeats).</div>
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<DateCreated><Year>2012</Year>
<Month>04</Month>
<Day>27</Day>
</DateCreated>
<DateCompleted><Year>2013</Year>
<Month>03</Month>
<Day>14</Day>
</DateCompleted>
<DateRevised><Year>2015</Year>
<Month>02</Month>
<Day>25</Day>
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<Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2105</ISSN>
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<PubDate><Year>2012</Year>
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<Title>BMC bioinformatics</Title>
<ISOAbbreviation>BMC Bioinformatics</ISOAbbreviation>
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<ArticleTitle>Ab initio detection of fuzzy amino acid tandem repeats in protein sequences.</ArticleTitle>
<Pagination><MedlinePgn>S8</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2105-13-S3-S8</ELocationID>
<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Tandem repetitions within protein amino acid sequences often correspond to regular secondary structures and form multi-repeat 3D assemblies of varied size and function. Developing internal repetitions is one of the evolutionary mechanisms that proteins employ to adapt their structure and function under evolutionary pressure. While there is keen interest in understanding such phenomena, detection of repeating structures based only on sequence analysis is considered an arduous task, since structure and function is often preserved even under considerable sequence divergence (fuzzy tandem repeats).</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">In this paper we present PTRStalker, a new algorithm for ab-initio detection of fuzzy tandem repeats in protein amino acid sequences. In the reported results we show that by feeding PTRStalker with amino acid sequences from the UniProtKB/Swiss-Prot database we detect novel tandemly repeated structures not captured by other state-of-the-art tools. Experiments with membrane proteins indicate that PTRStalker can detect global symmetries in the primary structure which are then reflected in the tertiary structure.</AbstractText>
<AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">PTRStalker is able to detect fuzzy tandem repeating structures in protein sequences, with performance beyond the current state-of-the art. Such a tool may be a valuable support to investigating protein structural properties when tertiary X-ray data is not available.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Pellegrini</LastName>
<ForeName>Marco</ForeName>
<Initials>M</Initials>
<AffiliationInfo><Affiliation>Istituto di Informatica e Telematica, CNR - Consiglio Nazionale delle Ricerche, Pisa I-56124, Italy. marco.pellegrini@iit.cnr.it</Affiliation>
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<Author ValidYN="Y"><LastName>Renda</LastName>
<ForeName>Maria Elena</ForeName>
<Initials>ME</Initials>
</Author>
<Author ValidYN="Y"><LastName>Vecchio</LastName>
<ForeName>Alessio</ForeName>
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Ab initio detection of fuzzy amino acid tandem repeats in protein sequences.

Ab initio detection of fuzzy amino acid tandem repeats in protein sequences.

Source :

Descripteurs français

English descriptors

Abstract

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

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki