ArticleActa crystallographica. Section D, Structural biology2020
The use of local structural similarity of distant homologues for crystallographic model building from a molecular-replacement solution.
Article in Acta crystallographica. Section D, Structural biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Crystal Structure of Caryolan-1-ol Synthase, a Sesquiterpene Synthase Catalyzing an Initial Anti-Markovnikov Cyclization Reaction.Biochemistry · 2024Article
- Advanced glycation end-product crosslinking activates a type VI secretion system phospholipase effector protein.Nature communications · 2024Article
- Modes and model building in SHELXE.Acta crystallographica. Section D, Structural biology · 2024Article
- Predicted models and CCP4.Acta crystallographica. Section D, Structural biology · 2023Article
- Structure of the photoreceptor synaptic assembly of the extracellular matrix protein pikachurin with the orphan receptor GPR179.Science signaling · 2023Article
- ModelCraft: an advanced automated model-building pipeline using Buccaneer.Acta crystallographica. Section D, Structural biology · 2022Article
- Structural basis of synergistic neutralization of Crimean-Congo hemorrhagic fever virus by human antibodies.Science (New York, N.Y.) · 2022Article
- Structural insights into 3Fe-4S ferredoxins diversity inFrontiers in molecular biosciences · 2022Article
- Article
- The accuracy of protein models automatically built into cryo-EM maps with ARP/wARP.Acta crystallographica. Section D, Structural biology · 2021Article
- Pairwise running of automated crystallographic model-building pipelines.Acta crystallographica. Section D, Structural biology · 2020Article
- SEQUENCE SLIDER: expanding polyalanine fragments for phasing with multiple side-chain hypotheses.Acta crystallographica. Section D, Structural biology · 2020Article
- ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation.Acta crystallographica. Section D, Structural biology · 2020Article
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7 authors.
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Abstract
The performance of automated protein model building usually decreases with resolution, mainly owing to the lower information content of the experimental data. This calls for a more elaborate use of the available structural information about macromolecules. Here, a new method is presented that uses structural homologues to improve the quality of protein models automatically constructed using ARP/wARP. The method uses local structural similarity between deposited models and the model being built, and results in longer main-chain fragments that in turn can be more reliably docked to the protein sequence. The application of the homology-based model extension method to the example of a CFA synthase at 2.7 Å resolution resulted in a more complete model with almost all of the residues correctly built and docked to the sequence. The method was also evaluated on 1493 molecular-replacement solutions at a resolution of 4.0 Å and better that were submitted to the ARP/wARP web service for model building. A significant improvement in the completeness and sequence coverage of the built models has been observed.
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