ArticleStructure (London, England : 1993)2019
Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides that Bind Anti-apoptotic Bfl-1 and Mcl-1.
Article in Structure (London, England : 1993), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 35 citations in OpenAlex.
- From atoms to fragments: a coarse representation for efficient and functional protein design.Bioinformatics (Oxford, England) · 2026Article
- The State-of-the-Art Overview to Application of Deep Learning in Accurate Protein Design and Structure Prediction.Topics in current chemistry (Cham) · 2024Review
- Peptides from human BNIP5 and PXT1 and non-native binders of pro-apoptotic BAK can directly activate or inhibit BAK-mediated membrane permeabilization.Structure (London, England : 1993) · 2023Article
- Rational design of Harakiri (HRK)-derived constrained peptides as BCL-xChemical communications (Cambridge, England) · 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
- Fragment-based computational design of antibodies targeting structured epitopes.Science advances · 2022Article
- Last but not least: BFL-1 as an emerging target for anti-cancer therapies.Biochemical Society transactions · 2022Review
- Tertiary motifs as building blocks for the design of protein-binding peptides.Protein science : a publication of the Protein Society · 2022Article
- Design of Protein Segments and Peptides for Binding to Protein Targets.Biodesign research · 2022Review
- Towards optimizing peptide-based inhibitors of protein-protein interactions: predictive saturation variation scanning (PreSaVS).RSC chemical biology · 2021Article
- Data-driven computational protein design.Current opinion in structural biology · 2021Review
- Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials.Nature communications · 2021Article
- Selective Affimers Recognise the BCL-2 Family Proteins BCL-xChembiochem : a European journal of chemical biology · 2021Article
- Allosteric cooperation in a de novo-designed two-domain protein.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- A general-purpose protein design framework based on mining sequence-structure relationships in known protein structures.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level.PLoS computational biology · 2019Article
- Advances in protein structure prediction and design.Nature reviews. Molecular cell biology · 2019Review
- Recent advances in de novo protein design: Principles, methods, and applications.The Journal of biological chemistryReview
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Understanding the relationship between protein sequence and structure well enough to design new proteins with desired functions is a longstanding goal in protein science. Here, we show that recurring tertiary structural motifs (TERMs) in the PDB provide rich information for protein-peptide interaction prediction and design. TERM statistics can be used to predict peptide binding energies for Bcl-2 family proteins as accurately as widely used structure-based tools. Furthermore, design using TERM energies (dTERMen) rapidly and reliably generates high-affinity peptide binders of anti-apoptotic proteins Bfl-1 and Mcl-1 with just 15%-38% sequence identity to any known native Bcl-2 family protein ligand. High-resolution structures of four designed peptides bound to their targets provide opportunities to analyze the strengths and limitations of the computational design method. Our results support dTERMen as a powerful approach that can complement existing tools for protein engineering.
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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.