The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Probing the role of packing specificity in protein design
Open accessAbstract
By using a protein-design algorithm that quantitatively considers side-chain packing, the effect of specific steric constraints on protein design was assessed in the core of the streptococcal protein G β1 domain. The strength of packing constraints used in the design was varied, resulting in core sequences that reflected differing amounts of packing specificity. The structural flexibility and stability of several of the designed proteins were experimentally determined and showed a trend from well-ordered to highly mobile structures as the degree of packing specificity in the design decreased. This trend both demonstrates that the inclusion of specific packing interactions is necessary for the design of native-like proteins and defines a useful range of packing specificity for the design algorithm. In addition, an analysis of the modeled protein structures suggested that penalizing for exposed hydrophobic surface area can improve design performance.
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Cites
A Switch Between Two-, Three-, and Four-stranded Coiled Coils in GCN4 Leucine Zipper Mutants
Harbury, P. B., Zhang, T., Kim, P. S., & Alber, T. (1993) · Science · doi:10.1126/science.8248779 · Cited by 1,490
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The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
Alford, R. F., Leaver-Fay, A., Jeliazkov, J. R., O’Meara, M. J., DiMaio, F. P., Park, H., Shapovalov, M. V., Renfrew, P. D., Mulligan, V. K., Kappel, K., et al. (2017) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.7b00125 · Cited by 1,532
Al-Lazikani, B., Jung, J., Xiang, Z., & Honig, B. (2001) · Current Opinion in Chemical Biology · doi:10.1016/s1367-5931(00)00164-2 · Cited by 316
De Novo Design of Helical Bundles as Models for Understanding Protein Folding and Function
Hill, R. B., Raleigh, D. P., Lombardi, A., & DeGrado, W. F. (2000) · Accounts of Chemical Research · doi:10.1021/ar970004h · Cited by 300
Perturbing the energy landscape for improved packing during computational protein design
Maguire, J. B., Haddox, H. K., Strickland, D., Halabiya, S. F., Coventry, B., Griffin, J. R., Pulavarti, S. V. S. R. K., Cummins, M., Thieker, D. F., Klavins, E., et al. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26030 · Cited by 169
Antibody affinity maturation by computational design
Kuroda, D., & Tsumoto, K. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-8648-4_2 · Cited by 26
Metadata
- Authors
- Dahiyat, B. I., & Mayo, S. L.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 1997-09-16
- Volume
- 94
- Issue
- 19
- Pages
- 10172-10177
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2154031461
- Cited by
- 251
- References
- 1
- FWCI
- 5.06
- Type
- journal article
- Language
- en
- Open access
- green
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- Dahiyat, B. I., & Mayo, S. L. (1997). Probing the role of packing specificity in protein design. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.94.19.10172
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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