ArticleProteins2011
RaptorX: exploiting structure information for protein alignment by statistical inference.
Article in Proteins, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 155 papers.
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Who cites it
155 citing papers in PubMed.
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- Deep learning methods for protein function prediction.Proteomics · 2025Review
- Graph Neural Network-Based Approaches for Protein Function Prediction.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Exploring the Synergistic Mechanism of AP2A2 Transcription Factor Inhibition via Molecular Modeling and Simulations as a Novel Computational Approach for Combating Breast Cancer: In Silico Interpretations.Molecular biotechnology · 2024Article
- Article
- AI-Driven Deep Learning Techniques in Protein Structure Prediction.International journal of molecular sciences · 2024Review
- Insights into structural vaccinology harnessed for universal coronavirus vaccine development.Clinical and experimental vaccine research · 2024Review
- Predicting therapeutic and side effects from drug binding affinities to human proteome structures.iScience · 2024Article
- A candidate sex determination locus in amphibians which evolved by structural variation between X- and Y-chromosomes.Nature communications · 2024Article
- The Oligomeric State of Vasorin in the Plasma Membrane Measured Non-Invasively by Quantitative Fluorescence Fluctuation Spectroscopy.International journal of molecular sciences · 2024Article
- Recent Progress of Protein Tertiary Structure Prediction.Molecules (Basel, Switzerland) · 2024Review
- Structural Analysis of Breast-Milk αInternational journal of molecular sciences · 2024Article
- Computational insight into stability-enhanced systems of anthocyanin with protein/peptide.Food chemistry. Molecular sciences · 2023Article
- Identification of Orbivirus Non-Structural Protein 5 (NS5), Its Role and Interaction with RNA/DNA in Infected Cells.International journal of molecular sciences · 2023Article
- Immunoinformatics Protocol to Design Multi-Epitope Subunit Vaccines.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Reference panel guided topological structure annotation of Hi-C data.Nature communications · 2022Article
- Immunoinformatics-guided designing and in silico analysis of epitope-based polyvalent vaccines against multiple strains of human coronavirus (HCoV).Expert review of vaccines · 2022Article
95 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
This work presents RaptorX, a statistical method for template-based protein modeling that improves alignment accuracy by exploiting structural information in a single or multiple templates. RaptorX consists of three major components: single-template threading, alignment quality prediction, and multiple-template threading. This work summarizes the methods used by RaptorX and presents its CASP9 result analysis, aiming to identify major bottlenecks with RaptorX and template-based modeling and hopefully directions for further study. Our results show that template structural information helps a lot with both single-template and multiple-template protein threading especially when closely-related templates are unavailable, and there is still large room for improvement in both alignment and template selection. The RaptorX web server is available at http://raptorx.uchicago.edu.
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Registered trials
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