ArticleProceedings of the National Academy of Sciences of the United States of America2010
Protein structure determination by exhaustive search of Protein Data Bank derived databases.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
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- CCP4 Cloud for structure determination and project management in macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2022Article
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- The crystal structure of vaccinia virus protein E2 and perspectives on the prediction of novel viral protein folds.The Journal of general virology · 2022Article
- Phasertng: directed acyclic graphs for crystallographic phasing.Acta crystallographica. Section D, Structural biology · 2021Article
- Crystal structure of the Rab-binding domain of Rab11 family-interacting protein 2.Acta crystallographica. Section F, Structural biology communications · 2020Article
- Using Phaser and ensembles to improve the performance of SIMBAD.Acta crystallographica. Section D, Structural biology · 2020Article
- Molecular replacement using structure predictions from databases.Acta crystallographica. Section D, Structural biology · 2019Article
- Universal fluorescent sensors of high-affinity iron transport, applied to ESKAPE pathogens.The Journal of biological chemistry · 2019Article
- High-resolution crystal structure of arthropod Eiger TNF suggests a mode of receptor engagement and altered surface charge within endosomes.Communications biology · 2019Article
- SIMBAD: a sequence-independent molecular-replacement pipeline.Acta crystallographica. Section D, Structural biology · 2018Article
- Recent developments in MrBUMP: better search-model preparation, graphical interaction with search models, and solution improvement and assessment.Acta crystallographica. Section D, Structural biology · 2018Article
- Review
- TonB-Dependent Heme/Hemoglobin Utilization by Caulobacter crescentus HutA.Journal of bacteriology · 2017Article
- Article
- Initiating heavy-atom-based phasing by multi-dimensional molecular replacement.Acta crystallographica. Section D, Structural biology · 2016Article
- Crystal Structure of a Hidden Protein, YcaC, a Putative Cysteine Hydrolase from Pseudomonas aeruginosa, with and without an Acrylamide Adduct.International journal of molecular sciences · 2015Article
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2 authors.
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Abstract
Parallel sequence and structure alignment tools have become ubiquitous and invaluable at all levels in the study of biological systems. We demonstrate the application and utility of this same parallel search paradigm to the process of protein structure determination, benefitting from the large and growing corpus of known structures. Such searches were previously computationally intractable. Through the method of Wide Search Molecular Replacement, developed here, they can be completed in a few hours with the aide of national-scale federated cyberinfrastructure. By dramatically expanding the range of models considered for structure determination, we show that small (less than 12% structural coverage) and low sequence identity (less than 20% identity) template structures can be identified through multidimensional template scoring metrics and used for structure determination. Many new macromolecular complexes can benefit significantly from such a technique due to the lack of known homologous protein folds or sequences. We demonstrate the effectiveness of the method by determining the structure of a full-length p97 homologue from Trichoplusia ni. Example cases with the MHC/T-cell receptor complex and the EmoB protein provide systematic estimates of minimum sequence identity, structure coverage, and structural similarity required for this method to succeed. We describe how this structure-search approach and other novel computationally intensive workflows are made tractable through integration with the US national computational cyberinfrastructure, allowing, for example, rapid processing of the entire Structural Classification of Proteins protein fragment database.
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