ArticleBioinformatics (Oxford, England)2017
Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Computational design and translational development of TCR-mimic scFv antibodies for peptide-HLA neoantigen targeting.npj drug discovery · 2026Review
- Highly Accurate and Efficient Deep Learning Paradigm for Full-Atom Protein Loop Modeling with KarmaLoop.Research (Washington, D.C.) · 2024Article
- Impaired proliferation and migration of HUVEC and melanoma cells by human anti-FGF2 mAbs derived from a murine hybridoma by guided selection.Bioengineered · 2023Article
- Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency.Briefings in bioinformatics · 2023Article
- Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens.Journal of chemical theory and computation · 2023Review
- Nanobodies: Robust miniprotein binders in biomedicine.Advanced drug delivery reviews · 2023Review
- Computational Modeling of Antibody and T-Cell Receptor (CDR3 Loops).Methods in molecular biology (Clifton, N.J.) · 2023Article
- Benchmarking the Accuracy of AlphaFold 2 in Loop Structure Prediction.Biomolecules · 2022Article
- Accurate positioning of functional residues with robotics-inspired computational protein design.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Article
- The Therapeutic Antibody Profiler for Computational Developability Assessment.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Structural studies of codeinone reductase reveal novel insights into aldo-keto reductase function in benzylisoquinoline alkaloid biosynthesis.The Journal of biological chemistry · 2021Article
- Selection and Modelling of a New Single-Domain Intrabody Against TDP-43.Frontiers in molecular biosciences · 2021Article
- ProMod3-A versatile homology modelling toolbox.PLoS computational biology · 2021Article
- Current approaches to flexible loop modeling.Current research in structural biology · 2021Review
- Germline-Dependent Antibody Paratope States and Pairing Specific VFrontiers in immunology · 2021Article
- Structural basis for antibiotic action of the BNature chemical biology · 2020Article
- Antibodies exhibit multiple paratope states influencing VCommunications biology · 2020Article
- Computational approaches to therapeutic antibody design: established methods and emerging trends.Briefings in bioinformatics · 2020Review
- How repertoire data are changing antibody science.The Journal of biological chemistry · 2020Review
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Authors and funding
8 authors.
Funding
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Abstract
Motivation: Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. Here, we present a novel method, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction. Results: We show that Sphinx is able to generate high-accuracy predictions and decoy sets enriched with near-native loop conformations, performing better than the ab initio algorithm on which it is based. In addition, it is able to provide predictions for every target, unlike some knowledge-based methods. Sphinx can be used successfully for the difficult problem of antibody H3 prediction, outperforming RosettaAntibody, one of the leading H3-specific ab initio methods, both in accuracy and speed. Availability and Implementation: Sphinx is available at http://opig.stats.ox.ac.uk/webapps/sphinx. Contact: deane@stats.ox.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online.
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