ArticleNucleic acids research2019
DaReUS-Loop: a web server to model multiple loops in homology models.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
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- 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
- Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency.Briefings in bioinformatics · 2023Article
- Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization.Journal of chemical information and modeling · 2023Article
- The ClusPro AbEMap web server for the prediction of antibody epitopes.Nature protocols · 2023Review
- AsiteDesign: a Semirational Algorithm for an Automated Enzyme Design.The journal of physical chemistry. B · 2023Article
- A human monoclonal antibody bivalently binding two different epitopes in streptococcal M protein mediates immune function.EMBO molecular medicine · 2023Article
- Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics.PLoS computational biology · 2023Article
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- ABCG2/BCRP transport mechanism revealed through kinetically excited targeted molecular dynamics simulations.Computational and structural biotechnology journal · 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
- Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology.PLoS computational biology · 2021Article
- Structural and Kinetic Insights Into the Molecular Basis of Salt Tolerance of the Short-Chain Glucose-6-Phosphate Dehydrogenase FromFrontiers in microbiology · 2021Article
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Authors and funding
6 authors.
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Abstract
Loop regions in protein structures often have crucial roles, and they are much more variable in sequence and structure than other regions. In homology modeling, this leads to larger deviations from the homologous templates, and loop modeling of homology models remains an open problem. To address this issue, we have previously developed the DaReUS-Loop protocol, leading to significant improvement over existing methods. Here, a DaReUS-Loop web server is presented, providing an automated platform for modeling or remodeling loops in the context of homology models. This is the first web server accepting a protein with up to 20 loop regions, and modeling them all in parallel. It also provides a prediction confidence level that corresponds to the expected accuracy of the loops. DaReUS-Loop facilitates the analysis of the results through its interactive graphical interface and is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/services/DaReUS-Loop/.
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