ArticleJournal of molecular biology2014
A "fuzzy"-logic language for encoding multiple physical traits in biomolecules.
Article in Journal of molecular biology, 2014. 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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Who cites it
16 citing papers in PubMed.
- Structural and biochemical insights into HCV envelope proteins for germline-targeting vaccines.PLoS pathogens · 2026Article
- Article
- Evolutionary paths that link orthogonal pairs of binding proteins.Cell systems · 2025Article
- Large-scale energy decomposition for the analysis of protein stability.Cell stress & chaperones · 2025Article
- Design of stimulus-responsive two-state hinge proteins.Science (New York, N.Y.) · 2023Article
- Assessing and enhancing foldability in designed proteins.Protein science : a publication of the Protein Society · 2022Article
- Article
- A biophysical model of viral escape from polyclonal antibodies.Virus evolution · 2022Article
- Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design.Biochemistry · 2021Review
- The AbDesign computational pipeline for modular backbone assembly and design of binders and enzymes.Protein science : a publication of the Protein Society · 2021Article
- Practically useful protein-design methods combining phylogenetic and atomistic calculations.Current opinion in structural biology · 2020Review
- Ultrahigh specificity in a network of computationally designed protein-interaction pairs.Nature communications · 2018Article
- Principles for computational design of binding antibodies.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Searching for the Pareto frontier in multi-objective protein design.Biophysical reviews · 2017Review
- Incorporating an allosteric regulatory site in an antibody through backbone design.Protein science : a publication of the Protein Society · 2017Article
- AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences.Proteins · 2015Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
To carry out their activities, biological macromolecules balance different physical traits, such as stability, interaction affinity, and selectivity. How such often opposing traits are encoded in a macromolecular system is critical to our understanding of evolutionary processes and ability to design new molecules with desired functions. We present a framework for constraining design simulations to balance different physical characteristics. Each trait is represented by the equilibrium fractional occupancy of the desired state relative to its alternatives, ranging from none to full occupancy, and the different traits are combined using Boolean operators to effect a "fuzzy"-logic language for encoding any combination of traits. In another paper, we presented a new combinatorial backbone design algorithm AbDesign where the fuzzy-logic framework was used to optimize protein backbones and sequences for both stability and binding affinity in antibody-design simulation. We now extend this framework and find that fuzzy-logic design simulations reproduce sequence and structure design principles seen in nature to underlie exquisite specificity on the one hand and multispecificity on the other hand. The fuzzy-logic language is broadly applicable and could help define the space of tolerated and beneficial mutations in natural biomolecular systems and design artificial molecules that encode complex characteristics.
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Registered trials
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