ArticlePLoS computational biology2021
Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
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- To pack or not to pack: revisiting protein side-chain packing in the post-AlphaFold era.Briefings in bioinformatics · 2025Article
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- Challenges and Solutions for Leave-One-Out Biosensor Design in the Context of a Rugged Fitness Landscape.Sensors (Basel, Switzerland) · 2024Article
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- Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies.bioRxiv : the preprint server for biology · 2023Article
- Exploiting Sequence-Dependent Rotamer Information in Global Optimization of Proteins.The journal of physical chemistry. B · 2022Article
- De novo design of protein homodimers containing tunable symmetric protein pockets.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Reconfigurable asymmetric protein assemblies through implicit negative design.Science (New York, N.Y.) · 2022Article
- Design of multi-scale protein complexes by hierarchical building block fusion.Nature communications · 2021Article
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2 authors.
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Abstract
In aqueous solution, polar groups make hydrogen bonds with water, and hence burial of such groups in the interior of a protein is unfavorable unless the loss of hydrogen bonds with water is compensated by formation of new ones with other protein groups. For this reason, buried "unsatisfied" polar groups making no hydrogen bonds are very rare in proteins. Efficiently representing the energetic cost of unsatisfied hydrogen bonds with a pairwise-decomposable energy term during protein design is challenging since whether or not a group is satisfied depends on all of its neighbors. Here we describe a method for assigning a pairwise-decomposable energy to sidechain rotamers such that following combinatorial sidechain packing, buried unsaturated polar atoms are penalized. The penalty can be any quadratic function of the number of unsatisfied polar groups, and can be computed very rapidly. We show that inclusion of this term in Rosetta sidechain packing calculations substantially reduces the number of buried unsatisfied polar groups.
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