ArticleScientific reports2018
DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- From reactants to products: computational methods for biosynthetic pathway design.Synthetic and systems biotechnology · 2025Review
- The hinge-engineered IgG1-IgG3 hybrid subclass IgGhNature communications · 2024Article
- A bispecific antibody approach for the potential prophylactic treatment of inherited bleeding disorders.Nature cardiovascular research · 2024Article
- Recent Advances in Protein Folding Pathway Prediction through Computational Methods.Current medicinal chemistry · 2024Review
- Highly Accurate and Efficient Deep Learning Paradigm for Full-Atom Protein Loop Modeling with KarmaLoop.Research (Washington, D.C.) · 2024Article
- Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization.Journal of chemical information and modeling · 2023Article
- Modeling Protein Complexes and Molecular Assemblies Using Computational Methods.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Benchmarking the Accuracy of AlphaFold 2 in Loop Structure Prediction.Biomolecules · 2022Article
- Modeling a unit cell: crystallographic refinement procedure using the biomolecular MD simulation platformIUCrJ · 2022Article
- InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps.Nucleic acids research · 2021Article
- Pepscan Approach for the Identification of Protein-Protein Interfaces: Lessons from Experiment.Biomolecules · 2021Article
- Current approaches to flexible loop modeling.Current research in structural biology · 2021Review
- Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology.PLoS computational biology · 2021Article
- The CH1α domain of mucosal gp41 IgA contributes to antibody specificity and antiviral functions in HIV-1 highly exposed Sero-Negative individuals.PLoS pathogens · 2020Article
- Structural proteomics, electron cryo-microscopy and structural modeling approaches in bacteria-human protein interactions.Medical microbiology and immunology · 2020Review
- Ten quick tips for homology modeling of high-resolution protein 3D structures.PLoS computational biology · 2020Article
- Article
- DaReUS-Loop: a web server to model multiple loops in homology models.Nucleic acids research · 2019Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite efforts during the past decades, loop modeling remains a difficult part of protein structure modeling. Several approaches have been developed in the framework of crystal structures. However, for homology models, the modeling of loops is still far from being solved. We propose DaReUS-Loop, a data-based approach that identifies loop candidates mining the complete set of experimental structures available in the Protein Data Bank. Candidate filtering relies on local conformation profile-profile comparison, together with physico-chemical scoring. Applied to three different template-based test sets, DaReUS-Loop shows significant increase in the number of high-accuracy loops, and significant enhancement for modeling long loops. A special advantage is that our method proposes a prediction confidence score that correlates well with the expected accuracy of the loops. Strikingly, over 50% of successful loop models are derived from unrelated proteins, indicating that fragments under similar constraints tend to adopt similar structure, beyond mere homology.
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