ArticlePLoS computational biology2015
Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- AI-driven rational design of promiscuous and selective plastic-binding peptides.Chemical science · 2025Article
- Deep learning-guided design of dynamic proteins.Science (New York, N.Y.) · 2025Article
- Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens.Journal of chemical theory and computation · 2023Review
- Improved HIV-1 neutralization breadth and potency of V2-apex antibodies by in silico design.Cell reports · 2023Article
- Design and discovery of metamorphic proteins.Current opinion in structural biology · 2022Review
- Design principles of protein switches.Current opinion in structural biology · 2022Review
- Computational redesign of a fluorogen activating protein with Rosetta.PLoS computational biology · 2021Article
- Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design.Biochemistry · 2021Review
- Parameters and determinants of responses to selection in antibody libraries.PLoS computational biology · 2021Article
- Rosetta design with co-evolutionary information retains protein function.PLoS computational biology · 2021Article
- Predicting susceptibility to SARS-CoV-2 infection based on structural differences in ACE2 across species.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2020Article
- Macromolecular modeling and design in Rosetta: recent methods and frameworks.Nature methods · 2020Review
- Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering.International journal of molecular sciences · 2020Review
- Protein design under competing conditions for the availability of amino acids.Scientific reports · 2020Article
- Multi-state design of flexible proteins predicts sequences optimal for conformational change.PLoS computational biology · 2020Article
- Multistate design of influenza antibodies improves affinity and breadth against seasonal viruses.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- iCFN: an efficient exact algorithm for multistate protein design.Bioinformatics (Oxford, England) · 2018Article
- Integrating linear optimization with structural modeling to increase HIV neutralization breadth.PLoS computational biology · 2018Article
- Searching for the Pareto frontier in multi-objective protein design.Biophysical reviews · 2017Review
- Rosetta:MSF: a modular framework for multi-state computational protein design.PLoS computational biology · 2017Article
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Authors and funding
4 authors.
Funding
Abstract
Computational protein design has found great success in engineering proteins for thermodynamic stability, binding specificity, or enzymatic activity in a 'single state' design (SSD) paradigm. Multi-specificity design (MSD), on the other hand, involves considering the stability of multiple protein states simultaneously. We have developed a novel MSD algorithm, which we refer to as REstrained CONvergence in multi-specificity design (RECON). The algorithm allows each state to adopt its own sequence throughout the design process rather than enforcing a single sequence on all states. Convergence to a single sequence is encouraged through an incrementally increasing convergence restraint for corresponding positions. Compared to MSD algorithms that enforce (constrain) an identical sequence on all states the energy landscape is simplified, which accelerates the search drastically. As a result, RECON can readily be used in simulations with a flexible protein backbone. We have benchmarked RECON on two design tasks. First, we designed antibodies derived from a common germline gene against their diverse targets to assess recovery of the germline, polyspecific sequence. Second, we design "promiscuous", polyspecific proteins against all binding partners and measure recovery of the native sequence. We show that RECON is able to efficiently recover native-like, biologically relevant sequences in this diverse set of protein complexes.
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