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Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin
Open accessAbstract
Proteins can be designed that bind to specific patches on target proteins to alter their subsequent interactions.
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“Binders have been generated starting from several computationally identified hotspot residues, which were then used to guide the positioning of naturally occurring protein scaffolds5.”
From Design of protein-binding proteins from the target structure alone (2022) · cites this paper as [5]
In the citing paper
“The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains a challenge1–5.”
From Design of protein-binding proteins from the target structure alone (2022) · cites this paper as [5]
In the citing paper
“The RIF approach improves on previous discrete interaction-sampling approaches5 by reducing the algorithmic complexity from O(N) or O(N2) to O(1) with respect to the number of side-chain–target interactions considered, thereby allowing for billions, rather than thousands, of potential interfaces to be considered.”
From Design of protein-binding proteins from the target structure alone (2022) · cites this paper as [5]
In the citing paper
“Protein1,5, peptide36 and small-molecule inhibitors37 have been designed to bind to the stem region of group 1 HA and neutralize influenza A viruses, but none recognize the group 2 HA.”
From Design of protein-binding proteins from the target structure alone (2022) · cites this paper as [5]
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Cites
PatchDock and SymmDock: servers for rigid and symmetric docking
Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki481 · Cited by 3,018
A Hot Spot of Binding Energy in a Hormone-Receptor Interface
Clackson, T., & Wells, J. A. (1995) · Science · doi:10.1126/science.7529940 · Cited by 1,987
The atomic structure of protein-protein recognition sites 1 1Edited by A. R. Fersht
Conte, L. L., Chothia, C., & Janin, J. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2439 · Cited by 1,967
Design of a Novel Globular Protein Fold with Atomic-Level Accuracy
Kuhlman, B. A., Dantas, G. A., Ireton, G. C., Varani, G., Stoddard, B. L., & Baker, D. A. (2003) · Science · doi:10.1126/science.1089427 · Cited by 1,666
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Ekiert, D. C., Bhabha, G., Elsliger, M.-A., Friesen, R. H. E., Jongeneelen, M., Throsby, M., Goudsmit, J., & Wilson, I. A. (2009) · Science · doi:10.1126/science.1171491 · Cited by 1,326
Self-citationGray, J. J., Moughon, S. E., Wang, C., Schueler‐Furman, O., Kuhlman, B. A., Rohl, C. A., & Baker, D. A. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00670-3 · Cited by 1,130
Self-citationSui, J., Hwang, W. C., Perez, S., Ge, W., Aird, D. R., Chen, L., Santelli, E., Stec, B., Cadwell, G., Ali, M., et al. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1566 · Cited by 1,128
Clinical Aspects of Pandemic 2009 Influenza A (H1N1) Virus Infection
Writing Committee of the WHO Consultation on Clinical Aspects of Pandemic (H1N1) 2009 Influenza (2010) · New England Journal of Medicine · doi:10.1056/nejmra1000449 · Cited by 1,056
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Das, R., & Baker, D. A. (2008) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.77.062906.171838 · Cited by 995
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Metadata
- Authors
- Fleishman, S. J., Whitehead, T. A., Ekiert, D. C., Dreyfus, C., Corn, J. E., Strauch, E.-M., Wilson, I. A., & Baker, D.
- Affiliations
- University of Washington (US)
- Scripps Research Institute (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Fleishman, Sarel J.
- Whitehead, Timothy A.
- Ekiert, Damian C.
- Baker, David
- ORCID
- Venue
- Science
- Published
- 2011-05-13
- Volume
- 332
- Issue
- 6031
- Pages
- 816-821
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC3164876
- OpenAlex
- W2049275721
- Cited by
- 585
- References
- 20
- Citations by year
- 2026: 15 · 2025: 23 · 2024: 22 · 2023: 26 · 2022: 21 · 2021: 28 · 2020: 24 · 2019: 41 · 2018: 32 · 2017: 44 · 2016: 42 · 2015: 37 · 2014: 61 · 2013: 87 · 2012: 62
- FWCI
- 29.89
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- National Cancer Institute (Y1-CO-1020)
- National Institute of General Medical Sciences (Y1-GM-1104, GM080209, T32GM080209)
- National Institute of Allergy and Infectious Diseases (U54AI057141, P01AI058113, AI057141, AI058113)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Health Sciences › Medicine › Epidemiology › Influenza Virus Research Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Keywords
- protein design, influenza hemagglutinin, affinity maturation
- MeSH terms
- Algorithms, Amino Acid Sequence, Binding Sites, Computer Simulation, Hydrogen Bonding, Hydrogen-Ion Concentration, Models, Molecular, Molecular Sequence Data, Mutation, Protein Binding, Protein Conformation, Proteins, Software, Protein Engineering, Protein Structure, Secondary, Peptide Library, Hemagglutinin Glycoproteins, Influenza Virus, Computational Biology, Protein Interaction Domains and Motifs, Hydrophobic and Hydrophilic Interactions
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