WALTZ-DB: a benchmark database of amyloidogenic hexapeptides.
Identifieur interne : 000100 ( Main/Exploration ); précédent : 000099; suivant : 000101WALTZ-DB: a benchmark database of amyloidogenic hexapeptides.
Auteurs : Jacinte Beerten [Royaume-Uni] ; Joost Van Durme [Royaume-Uni] ; Rodrigo Gallardo [Royaume-Uni] ; Emidio Capriotti [Royaume-Uni] ; Louise Serpell [Royaume-Uni] ; Frederic Rousseau [Royaume-Uni] ; Joost Schymkowitz [Royaume-Uni]Source :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2015.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Amyloid, Oligopeptides.
- chemical , ultrastructure : Amyloid.
- Algorithms, Amino Acid Sequence, Databases, Protein.
Abstract
Accurate prediction of amyloid-forming amino acid sequences remains an important challenge. We here present an online database that provides open access to the largest set of experimentally characterized amyloid forming hexapeptides. To this end, we expanded our previous set of 280 hexapeptides used to develop the Waltz algorithm with 89 peptides from literature review and by systematic experimental characterisation of the aggregation of 720 hexapeptides by transmission electron microscopy, dye binding and Fourier transform infrared spectroscopy. This brings the total number of experimentally characterized hexapeptides in the WALTZ-DB database to 1089, of which 244 are annotated as positive for amyloid formation.
DOI: 10.1093/bioinformatics/btv027
PubMed: 25600945
Affiliations:
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last="Beerten">Jacinte Beerten</name><affiliation wicri:level="1"><nlm:affiliation>VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG</wicri:regionArea><wicri:noRegion>East Sussex BN1 9QG</wicri:noRegion></affiliation></author><author><name sortKey="Van Durme, Joost" sort="Van Durme, Joost" uniqKey="Van Durme J" first="Joost" last="Van Durme">Joost Van Durme</name><affiliation wicri:level="1"><nlm:affiliation>VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG</wicri:regionArea><wicri:noRegion>East Sussex BN1 9QG</wicri:noRegion></affiliation></author><author><name sortKey="Gallardo, Rodrigo" sort="Gallardo, Rodrigo" uniqKey="Gallardo R" first="Rodrigo" last="Gallardo">Rodrigo Gallardo</name><affiliation wicri:level="1"><nlm:affiliation>VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG</wicri:regionArea><wicri:noRegion>East Sussex BN1 9QG</wicri:noRegion></affiliation></author><author><name sortKey="Capriotti, Emidio" sort="Capriotti, Emidio" uniqKey="Capriotti E" first="Emidio" last="Capriotti">Emidio Capriotti</name><affiliation wicri:level="1"><nlm:affiliation>VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG</wicri:regionArea><wicri:noRegion>East Sussex BN1 9QG</wicri:noRegion></affiliation></author><author><name sortKey="Serpell, Louise" sort="Serpell, Louise" uniqKey="Serpell L" first="Louise" last="Serpell">Louise Serpell</name><affiliation wicri:level="1"><nlm:affiliation>VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG</wicri:regionArea><wicri:noRegion>East Sussex BN1 9QG</wicri:noRegion></affiliation></author><author><name sortKey="Rousseau, Frederic" sort="Rousseau, Frederic" uniqKey="Rousseau F" first="Frederic" last="Rousseau">Frederic Rousseau</name><affiliation wicri:level="1"><nlm:affiliation>VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG</wicri:regionArea><wicri:noRegion>East Sussex BN1 9QG</wicri:noRegion></affiliation></author><author><name sortKey="Schymkowitz, Joost" sort="Schymkowitz, Joost" uniqKey="Schymkowitz J" first="Joost" last="Schymkowitz">Joost Schymkowitz</name><affiliation wicri:level="1"><nlm:affiliation>VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK VIB Switch Laboratory, Leuven, Belgium, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box 802, Leuven, Belgium, Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA and School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG</wicri:regionArea><wicri:noRegion>East Sussex BN1 9QG</wicri:noRegion></affiliation></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Amino Acid Sequence</term><term>Amyloid (chemistry)</term><term>Amyloid (ultrastructure)</term><term>Databases, Protein</term><term>Oligopeptides (chemistry)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Amyloid</term><term>Oligopeptides</term></keywords><keywords scheme="MESH" type="chemical" qualifier="ultrastructure" xml:lang="en"><term>Amyloid</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Amino Acid Sequence</term><term>Databases, Protein</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Accurate prediction of amyloid-forming amino acid sequences remains an important challenge. We here present an online database that provides open access to the largest set of experimentally characterized amyloid forming hexapeptides. To this end, we expanded our previous set of 280 hexapeptides used to develop the Waltz algorithm with 89 peptides from literature review and by systematic experimental characterisation of the aggregation of 720 hexapeptides by transmission electron microscopy, dye binding and Fourier transform infrared spectroscopy. This brings the total number of experimentally characterized hexapeptides in the WALTZ-DB database to 1089, of which 244 are annotated as positive for amyloid formation.</div></front></TEI><affiliations><list><country><li>Royaume-Uni</li></country></list><tree><country name="Royaume-Uni"><noRegion><name sortKey="Beerten, Jacinte" sort="Beerten, Jacinte" uniqKey="Beerten J" first="Jacinte" last="Beerten">Jacinte Beerten</name></noRegion><name sortKey="Capriotti, Emidio" sort="Capriotti, Emidio" uniqKey="Capriotti E" first="Emidio" last="Capriotti">Emidio Capriotti</name><name sortKey="Gallardo, Rodrigo" sort="Gallardo, Rodrigo" uniqKey="Gallardo R" first="Rodrigo" last="Gallardo">Rodrigo Gallardo</name><name sortKey="Rousseau, Frederic" sort="Rousseau, Frederic" uniqKey="Rousseau F" first="Frederic" last="Rousseau">Frederic Rousseau</name><name sortKey="Schymkowitz, Joost" sort="Schymkowitz, Joost" uniqKey="Schymkowitz J" first="Joost" last="Schymkowitz">Joost Schymkowitz</name><name sortKey="Serpell, Louise" sort="Serpell, Louise" uniqKey="Serpell L" first="Louise" last="Serpell">Louise Serpell</name><name sortKey="Van Durme, Joost" sort="Van Durme, Joost" uniqKey="Van Durme J" first="Joost" last="Van Durme">Joost Van Durme</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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