The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing
Open accessAbstract
Summary We show that amino acid co-variation in proteins, extracted from the evolutionary sequence record, can be used to fold transmembrane proteins. We use this technique to predict previously unknown, 3D structures for 11 transmembrane proteins (with up to 14 helices) from their sequences alone. The prediction method (EVfold_membrane), applies a maximum entropy approach to infer evolutionary co-variation in pairs of sequence positions within a protein family and then generates all-atom models with the derived pairwise distance constraints. We benchmark the approach with blinded, de novo computation of known transmembrane protein structures from 23 families, demonstrating unprecedented accuracy of the method for large transmembrane proteins. We show how the method can predict oligomerization, functional sites, and conformational changes in transmembrane proteins. With the rapid rise in large-scale sequencing, more accurate and more comprehensive information on evolutionary constraints can be decoded from genetic variation, greatly expanding the repertoire of transmembrane proteins amenable to modelling by this method.
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Self-citationProtein Structure Comparison by Alignment of Distance Matrices
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“Thepre-dicted structures of five of the proteins had similar folds to other known3Dmembraneproteinstructures(Figure2C)despitenegli-gible sequence similarity, a recurring theme seen in structural genomics and earlier work (Holm and Sander, 1993; Murzin, 1993).”
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Self-citationProtein 3D Structure Computed from Evolutionary Sequence Variation
Marks, D. S., Colwell, L. J., Sheridan, R., Hopf, T. A., Pagnani, A., Zecchina, R., & Sander, C. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028766 · Cited by 1,144
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Metadata
- Authors
- Hopf, T. A., Colwell, L. J., Sheridan, R., Rost, B., Sander, C., & Marks, D. S.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2012-06
- Volume
- 149
- Issue
- 7
- Pages
- 1607-1621
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2051545676
- Cited by
- 512
- References
- 12
- FWCI
- 19.52
- Type
- journal article
- Language
- en
- Open access
- bronze
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