ArticleSpringerPlus2016
Structural homology guided alignment of cysteine rich proteins.
Article in SpringerPlus, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 21 citations in OpenAlex.
- Article
- Hyperpolarisation of Mitochondrial Membranes Is a Critical Component of the Antifungal Mechanism of the Plant Defensin, Ppdef1.Journal of fungi (Basel, Switzerland) · 2024Article
- Structural and functional basis of VLDLR receptor usage by Eastern equine encephalitis virus.bioRxiv : the preprint server for biology · 2023Article
- Killer Knots: Molecular Evolution of Inhibitor Cystine Knot Toxins in Wandering Spiders (Araneae: Ctenidae).Toxins · 2023Article
- Comprehensive computational analysis of the SRK-SP11 molecular interaction underlying self-incompatibility in Brassicaceae using improved structure prediction for cysteine-rich proteins.Computational and structural biotechnology journal · 2023Article
- Orientational Preferences of GPI-Anchored Ly6/uPAR Proteins.International journal of molecular sciences · 2022Article
- Histidine-Rich Defensins from theJournal of fungi (Basel, Switzerland) · 2020Article
- Orientation-dependent toxic effect of human papillomavirus type 33 long control region DNA in Escherichia coli cells.Virus genes · 2020Article
- Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group.Journal of visualized experiments : JoVE · 2017Article
- Convergent evolution of defensin sequence, structure and function.Cellular and molecular life sciences : CMLS · 2017Review
- AlignStat: a web-tool and R package for statistical comparison of alternative multiple sequence alignments.BMC bioinformatics · 2016Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCysteine rich protein families are notoriously difficult to align due to low sequence identity and frequent insertions and deletions.
resultsHere we present an alignment method that ensures homologous cysteines align by assigning a unique 10 amino acid barcode to those identified as structurally homologous by the DALI webserver. The free inter-cysteine regions of the barcoded sequences can then be aligned using any standard algorithm. Finally the barcodes are replaced with the original columns to yield an alignment which requires the minimum of manual refinement.
conclusionsUsing structural homology information to constrain sequence alignments allows the alignment of highly divergent, repetitive sequences that are poorly dealt with by existing algorithms. Tools are provided to perform this method online using the CysBar web-tool (http://CysBar.science.latrobe.edu.au) and offline (python script available from http://github.com/ts404/CysBar).
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