WALTZ-DB: a benchmark database of amyloidogenic hexapeptides

Jacinte Beerten; Joost Van Durme; Rodrigo Gallardo; Emidio Capriotti; Louise Serpell; Frederic Rousseau; Joost Schymkowitz

doi:10.1093/bioinformatics/btv027

WALTZ-DB: a benchmark database of amyloidogenic hexapeptides

Bioinformatics. 2015 May 15;31(10):1698-700. doi: 10.1093/bioinformatics/btv027. Epub 2015 Jan 18.

Authors

Jacinte Beerten¹, Joost Van Durme¹, Rodrigo Gallardo¹, Emidio Capriotti², Louise Serpell³, Frederic Rousseau¹, Joost Schymkowitz¹

Affiliations

¹ 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.
² 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.
³ 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.

PMID: 25600945
DOI: 10.1093/bioinformatics/btv027

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Amino Acid Sequence
Amyloid / chemistry*
Amyloid / ultrastructure
Databases, Protein*
Oligopeptides / chemistry*

Substances

Amyloid
Oligopeptides

Grants and funding

MR/K022105/1/MRC_/Medical Research Council/United Kingdom