ArticleProceedings of the National Academy of Sciences of the United States of America2018
Peptide design by optimization on a data-parameterized protein interaction landscape.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
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Who cites it
33 citing papers in PubMed.
- De Novo-Designed Bifunctional Proteins for Targeted Protein Degradation.Journal of the American Chemical Society · 2026Article
- Screening of the Prodiginine Molecules as BH3-mimetics against the Developed Bcl-2 Antiapoptotic Chemotherapeutic Resistance: A Molecular Docking and ADMET Study Supported by Molecular Dynamics Simulations.Current computer-aided drug design · 2026Article
- Screening macrocyclic peptide libraries by yeast display allows control of selection process and affinity ranking.Nature communications · 2025Article
- In silico screening of protein-binding peptides with an application to developing peptide inhibitors against antibiotic resistance.PNAS nexus · 2024Article
- Deep neural networks for predicting the affinity landscape of protein-protein interactions.iScience · 2024Article
- Cold Spot SCANNER: Colab Notebook for predicting cold spots in protein-protein interfaces.BMC bioinformatics · 2024Article
- Peptide-based allosteric inhibitor targets TNFR1 conformationally active region and disables receptor-ligand signaling complex.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Machine learning to predict continuous protein properties from binary cell sorting data and map unseen sequence space.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Design of target specific peptide inhibitors using generative deep learning and molecular dynamics simulations.Nature communications · 2024Article
- Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data.Bioinformatics (Oxford, England) · 2023Article
- Protein engineering via sequence-performance mapping.Cell systems · 2023Review
- Rapid Evaluation of Staple Placement in Stabilized α Helices Using Bacterial Surface Display.ACS chemical biology · 2023Article
- Mutational scan inferred binding energetics and structure in intrinsically disordered protein CcdA.Protein science : a publication of the Protein Society · 2023Article
- Titrating Avidity of Yeast-Displayed Proteins Using a Transcriptional Regulator.ACS synthetic biology · 2023Article
- Neural network-derived Potts models for structure-based protein design using backbone atomic coordinates and tertiary motifs.Protein science : a publication of the Protein Society · 2023Article
- Tertiary motifs as building blocks for the design of protein-binding peptides.Protein science : a publication of the Protein Society · 2022Article
- Multiplexed Small-Molecule-Ligand Binding Assays by Affinity Labeling and DNA Sequence Analysis.Angewandte Chemie (International ed. in English) · 2022Article
- Design of Protein Segments and Peptides for Binding to Protein Targets.Biodesign research · 2022Review
- Lessons in Organic Fluorescent Probe Discovery.Chembiochem : a European journal of chemical biology · 2021Review
- Towards optimizing peptide-based inhibitors of protein-protein interactions: predictive saturation variation scanning (PreSaVS).RSC chemical biology · 2021Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Many applications in protein engineering require optimizing multiple protein properties simultaneously, such as binding one target but not others or binding a target while maintaining stability. Such multistate design problems require navigating a high-dimensional space to find proteins with desired characteristics. A model that relates protein sequence to functional attributes can guide design to solutions that would be hard to discover via screening. In this work, we measured thousands of protein-peptide binding affinities with the high-throughput interaction assay amped SORTCERY and used the data to parameterize a model of the alpha-helical peptide-binding landscape for three members of the Bcl-2 family of proteins: Bcl-x
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.