ArticleBioinformatics (Oxford, England)2010
Low-homology protein threading.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Article
- Yaravirus brasiliense genomic structure analysis and its possible influence on the metabolism.Genetics and molecular biology · 2025Article
- Structure prediction of alternative protein conformations.Nature communications · 2024Article
- Optimal trade-off control in machine learning-based library design, with application to adeno-associated virus (AAV) for gene therapy.Science advances · 2024Article
- Contact-Assisted Threading in Low-Homology Protein Modeling.Methods in molecular biology (Clifton, N.J.) · 2023Article
- From Genome Mining to Protein Engineering: A Structural Bioinformatics Route.Methods in molecular biology (Clifton, N.J.) · 2023Article
- FVIII inhibitors display FV-neutralizing activity in the prothrombin time assay.Journal of thrombosis and haemostasis : JTH · 2021Article
- Article
- Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading.Frontiers in molecular biosciences · 2021Review
- Evaluating the significance of contact maps in low-homology protein modeling using contact-assisted threading.Scientific reports · 2020Article
- A Novel Insecticidal Spider Peptide that Affects the Mammalian Voltage-Gated Ion Channel hKv1.5.Frontiers in pharmacology · 2020Article
- Improved homology modeling of the human & rat EPBMC molecular and cell biology · 2019Article
- Article
- Protein threading using residue co-variation and deep learning.Bioinformatics (Oxford, England) · 2018Article
- The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification.Microbiome · 2018Article
- Rapid and reliable protein structure determination via chemical shift threading.Journal of biomolecular NMR · 2018Article
- Protein alignment based on higher order conditional random fields for template-based modeling.PloS one · 2018Article
- Conservation and diversification of small RNA pathways within flatworms.BMC evolutionary biology · 2017Article
- Role of Structural Bioinformatics in Drug Discovery by Computational SNP Analysis: Analyzing Variation at the Protein Level.Global heart · 2017Review
- Molecular Modeling of Myrosinase from Brassica oleracea: A Structural Investigation of Sinigrin Interaction.Genes · 2015Article
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Abstract
motivationThe challenge of template-based modeling lies in the recognition of correct templates and generation of accurate sequence-template alignments. Homologous information has proved to be very powerful in detecting remote homologs, as demonstrated by the state-of-the-art profile-based method HHpred. However, HHpred does not fare well when proteins under consideration are low-homology. A protein is low-homology if we cannot obtain sufficient amount of homologous information for it from existing protein sequence databases.
resultsWe present a profile-entropy dependent scoring function for low-homology protein threading. This method will model correlation among various protein features and determine their relative importance according to the amount of homologous information available. When proteins under consideration are low-homology, our method will rely more on structure information; otherwise, homologous information. Experimental results indicate that our threading method greatly outperforms the best profile-based method HHpred and all the top CASP8 servers on low-homology proteins. Tested on the CASP8 hard targets, our threading method is also better than all the top CASP8 servers but slightly worse than Zhang-Server. This is significant considering that Zhang-Server and other top CASP8 servers use a combination of multiple structure-prediction techniques including consensus method, multiple-template modeling, template-free modeling and model refinement while our method is a classical single-template-based threading method without any post-threading refinement.
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