ArticleProtein science : a publication of the Protein Society2008
Novel protein folds and their nonsequential structural analogs.
Article in Protein science : a publication of the Protein Society, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed.
- epLSAP-Align: a non-sequential protein structural alignment solver with entropy-regularized partial linear sum assignment problem formulation.Bioinformatics (Oxford, England) · 2025Article
- Identifying Metal Binding Sites in Proteins Using Homologous Structures, the MADE Approach.Journal of chemical information and modeling · 2023Article
- SeqCP: A sequence-based algorithm for searching circularly permuted proteins.Computational and structural biotechnology journal · 2023Article
- A unified approach to sequential and non-sequential structure alignment of proteins, RNAs, and DNAs.iScience · 2022Article
- GADP-align: A genetic algorithm and dynamic programming-based method for structural alignment of proteins.BioImpacts : BI · 2021Article
- Non-sequential protein structure alignment by conformational space annealing and local refinement.PloS one · 2019Article
- Comparative Protein Structure Modeling Using MODELLER.Current protocols in bioinformatics · 2016Article
- Protein rethreading: A novel approach to protein design.Scientific reports · 2016Article
- Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner.BMC bioinformatics · 2016Article
- How a spatial arrangement of secondary structure elements is dispersed in the universe of protein folds.PloS one · 2014Article
- BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry.BMC structural biology · 2013Article
- Dipeptidyl peptidase IV is a human and murine neutrophil chemorepellent.Journal of immunology (Baltimore, Md. : 1950) · 2013Article
- MICAN: a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C(α) only models, Alternative alignments, and Non-sequential alignments.BMC bioinformatics · 2013Article
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- Implementation of a parallel protein structure alignment service on cloud.International journal of genomics · 2013Article
- Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility.PloS one · 2013Article
- Structure of a tetrameric galectin from Cinachyrella sp. (ball sponge).Acta crystallographica. Section D, Biological crystallography · 2012Article
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- The phylogenomic roots of modern biochemistry: origins of proteins, cofactors and protein biosynthesis.Journal of molecular evolution · 2012Article
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2 authors.
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Abstract
Newly determined protein structures are classified to belong to a new fold, if the structures are sufficiently dissimilar from all other so far known protein structures. To analyze structural similarities of proteins, structure alignment tools are used. We demonstrate that the usage of nonsequential structure alignment tools, which neglect the polypeptide chain connectivity, can yield structure alignments with significant similarities between proteins of known three-dimensional structure and newly determined protein structures that possess a new fold. The recently introduced protein structure alignment tool, GANGSTA, is specialized to perform nonsequential alignments with proper assignment of the secondary structure types by focusing on helices and strands only. In the new version, GANGSTA+, the underlying algorithms were completely redesigned, yielding enhanced quality of structure alignments, offering alignment against a larger database of protein structures, and being more efficient. We applied DaliLite, TM-align, and GANGSTA+ on three protein crystal structures considered to be novel folds. Applying GANGSTA+ to these novel folds, we find proteins in the ASTRAL40 database, which possess significant structural similarities, albeit the alignments are nonsequential and in some cases involve secondary structure elements aligned in reverse orientation. A web server is available at http://agknapp.chemie.fu-berlin.de/gplus for pairwise alignment, visualization, and database comparison.
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