ArticleActa crystallographica. Section D, Structural biology2022
ModelCraft: an advanced automated model-building pipeline using Buccaneer.
Article in Acta crystallographica. Section D, Structural biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed.
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- Dual function of ERH in primary miRNA biogenesis.Nucleic acids research · 2026Article
- Structure determination and dual targeting of a plant TACO1 identifies its ancient role as an organelle translation regulator.bioRxiv : the preprint server for biology · 2026Article
- Crystal structure of a cold-active arginase from Glaciozyma antarctica.Acta crystallographica. Section F, Structural biology communications · 2026Article
- Unlocking the secrets of SARS-CoV-2 nsp3 by combining experiments with AlphaFold2 domain prediction.Life science alliance · 2026Article
- AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network.Nature methods · 2026Article
- Crystallization and 1.6 Å resolution crystal structure of an acylated GLP-1/GIP analogue peptide.Acta crystallographica. Section F, Structural biology communications · 2026Article
- A milestone in C4 carbon concentration mechanism evolution: structural remodeling of NADP-malic enzyme in Poaceae.Molecular biology and evolution · 2026Article
- Structural and Functional Analysis of GGPPS Inhibition as a Therapeutic Mechanism for Acute Myeloid Leukemia (AML).Research square · 2025Article
- Extracellular vesicle-linked vitamin B12 acquisition via novel binding proteins in Bacteroides thetaiotaomicron.The Biochemical journal · 2025Article
- A role of pigment epithelium-derived factor in zinc-mediated mechanism of neurodegeneration in glaucoma.Communications biology · 2025Article
- Project automation in CCP4 Cloud: Enabling customization and high-throughput efficiency.Protein science : a publication of the Protein Society · 2025Article
- Mechanism and application of thiol-disulfide redox biosensors with a fluorescence-lifetime readout.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Slice'N'Dice: maximizing the value of predicted models for structural biologists.Acta crystallographica. Section D, Structural biology · 2025Article
- Structural basis for membrane association and catalysis by phosphatidylserine synthase inScience advances · 2024Article
- A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.Nature communications · 2024Article
- EF-P and its paralog EfpL (YeiP) differentially control translation of proline-containing sequences.Nature communications · 2024Article
- The success rate of processed predicted models in molecular replacement: implications for experimental phasing in the AlphaFold era.Acta crystallographica. Section D, Structural biology · 2024Article
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Abstract
Interactive model building can be a difficult and time-consuming step in the structure-solution process. Automated model-building programs such as Buccaneer often make it quicker and easier by completing most of the model in advance. However, they may fail to do so with low-resolution data or a poor initial model or map. The Buccaneer pipeline is a relatively simple program that iterates Buccaneer with REFMAC to refine the model and update the map. A new pipeline called ModelCraft has been developed that expands on this to include shift-field refinement, machine-learned pruning of incorrect residues, classical density modification, addition of water and dummy atoms, building of nucleic acids and final rebuilding of side chains. Testing was performed on 1180 structures solved by experimental phasing, 1338 structures solved by molecular replacement using homologues and 2030 structures solved by molecular replacement using predicted AlphaFold models. Compared with the previous Buccaneer pipeline, ModelCraft increased the mean completeness of the protein models in the experimental phasing cases from 91% to 95%, the molecular-replacement cases from 50% to 78% and the AlphaFold cases from 82% to 91%.
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