ArticleActa crystallographica. Section D, Structural biology2021
Vagabond: bond-based parametrization reduces overfitting for refinement of proteins.
Article in Acta crystallographica. Section D, Structural biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed.
- Calculation of minimum energy pathways in transport proteins.Communications chemistry · 2025Article
- Probing the modulation of enzyme kinetics by multi-temperature, time-resolved serial crystallography.Nature communications · 2025Article
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- Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM.bioRxiv : the preprint server for biology · 2024Article
- FLEXR: automated multi-conformer model building using electron-density map sampling.Acta crystallographica. Section D, Structural biology · 2023Article
- Torsion angles to map and visualize the conformational space of a protein.Protein science : a publication of the Protein Society · 2023Article
- Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data.Methods in enzymology · 2023Article
- Improving sampling of crystallographic disorder in ensemble refinement.Acta crystallographica. Section D, Structural biology · 2021Article
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Abstract
Structural biology methods have delivered over 150 000 high-resolution structures of macromolecules, which have fundamentally altered our understanding of biology and our approach to developing new medicines. However, the description of molecular flexibility is instrinsically flawed and in almost all cases, regardless of the experimental method used for structure determination, there remains a strong overfitting bias during molecular model building and refinement. In the worst case this can lead to wholly incorrect structures and thus incorrect biological interpretations. Here, by reparametrizing the description of these complex structures in terms of bonds rather than atomic positions, and by modelling flexibility using a deterministic ensemble of structures, it is demonstrated that structures can be described using fewer parameters than in conventional refinement. The current implementation, applied to X-ray diffraction data, significantly reduces the extent of overfitting, allowing the experimental data to reveal more biological information in electron-density maps.
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