De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity
By Scott E. Boyken, Zibo Chen, Benjamin Groves, Robert A. Langan, G. Oberdorfer, Alex Ford, Jason M. Gilmore, Chunfu Xu, Frank DiMaio, J. H. Pereira and 4 more. 2016
295 citations recorded by the source corpus.
Subfields: Molecular Biology
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In Molecular Biology
- David Baker
- Robin Pearce
- Yang Zhang
- Po-Ssu Huang
- Frank DiMaio
- Tanja Kortemme
- Enrique Marcos
- Raphael R. Eguchi
Citations in the corpus
- Energy-based models for atomic-resolution protein conformations (2020, background): “Such features have been shown to have important roles in protein structure and function (Guo & Salahub, 1998; Redzic & Bowler, 2005; Livesay et al., 2008), and are important in protein design (Boyken et al., 2016).”
- Protein sequence design with a learned potential (2020, background): “incur an entropic penalty as a result of solvent ordering under the hydrophobic effect and an enthalpic penalty from disrupting hydrogen bonding between polar solvent molecules [71, 72, 73], making it energetically favorable to place polar residues at solvent-accessible positions and apolar residues”
- Enhancing structure prediction and design of soluble and membrane proteins with explicit solvent-protein interactions (2017, background): “Ions perturb bulk water properties through strong charge-dipole interactions (Chen et al., 2016).”
- Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design (2018, methodology): “…uses a new data structure called HbondGraph that includes nodes for each rotamer, as well as atom-level information for each hydrogen bond, enabling more efficient organization and lookup as compared to the graph used by the original implementation of HBNet, which has been described previously 26 .”
- The coming of age of de novo protein design (2016, background): “In the past year, it has become possible to design with atomic-level accuracy extensive networks of hydrogen bonds in which almost all of the donors and acceptors are satisfied 63 .”