ArticleNature2025
One-shot design of functional protein binders with BindCraft.
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Article in Nature, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 165 papers.
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165citing papers in PubMed
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165 citing papers in PubMed.
- Artificial intelligence-assisted design of self-assembling peptide hydrogels for neural regeneration: Principles and opportunities.Bioactive materials · 2027Review
- Solid-state nanopore sensing: the next workhorse of biophysical characterization.Nature methods · 2026Review
- Better antibodies, better science.PLoS biology · 2026Article
- Degrading GPX4 via Biomimetic Nanoparticle-Mediated In Situ Synthesis of Deep-Learning-Designed Binder-Degron Chimeras for Prostate Cancer Therapy.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Latent generative search unlocks de novo design of untapped biomolecular interactions at scale.bioRxiv : the preprint server for biology · 2026Article
- ModelCIF Update: Supporting Emerging Classes of Computational Macromolecular Models.Journal of molecular biology · 2026Article
- Molecular dockingDigital discovery · 2026Article
- Defining attributes of effective binders for AI-assisted CAR design.Nature biomedical engineering · 2026Article
- Article
- De novo generation and computational screening of dual-targeting short peptide inhibitors against PBP2b and PBP2x in drug-resistant Streptococcus Pneumoniae.Molecular diversity · 2026Article
- Surf2Spot: a surface-informed geometry-aware model for predicting partner-independent binder and nanobody design hotspots.Briefings in bioinformatics · 2026Article
- Aligning protein-generative models to experimental fitness with ProteinDPO.Nature methods · 2026Article
- Solute carrier membrane transporters: emerging targets in CNS disorders.Nature reviews. Drug discovery · 2026Review
- Plant immune receptors built in silico and evolved in vivo.Nature plants · 2026Article
- Structural T-Cell Receptor Analysis in the Age of Machine Learning.Immunological reviews · 2026Review
- HighFold4: extending AlphaFold3 to accurate cyclic peptide conformation prediction via custom chemical connectivity.Briefings in bioinformatics · 2026Article
- Design of peptides with noncanonical amino acids using flow matching.Bioinformatics (Oxford, England) · 2026Article
- Targeting CDKs in the RNAPII transcription cycle.Nature reviews. Drug discovery · 2026Review
- AI-enabled discovery and biochemical optimization of minibinders targeting cancer cell-surface proteins.Nature communications · 2026Article
- Accelerating protein design by scaling experimental characterization.Nature communications · 2026Article
105 more citing papers are in PubMed but not listed here.
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Authors and funding
29 authors.
Martin Pacesa *Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland. martin.pacesa@epfl.ch.ORCID 0000-0003-1560-5769
Lennart Nickel *Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.ORCID 0000-0001-5535-4402
Christian Schellhaas *Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.ORCID 0000-0001-7367-1620
Joseph SchmidtLaboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.ORCID 0009-0002-7512-1563
Ekaterina PyatovaLaboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Lucas KisslingInstitute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.
Patrick BarendseLaboratory of Biochemistry, Wageningen University, Wageningen, the Netherlands.ORCID 0000-0002-6332-354X
Jagrity ChoudhuryDepartment of Structural Biology, University at Buffalo, Buffalo, NY, USA.
Srajan KapoorDepartment of Structural Biology, University at Buffalo, Buffalo, NY, USA.
Ana Alcaraz-SernaDivision of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
Yehlin ChoMassachusetts Institute of Technology, Cambridge, MA, USA.
Kourosh H GhamaryVisterra Inc., Waltham, MA, USA.
Laura VinuéVisterra Inc., Waltham, MA, USA.
Brahm J YachninVisterra Inc., Waltham, MA, USA.ORCID 0000-0001-6812-6329
Andrew M WollacottVisterra Inc., Waltham, MA, USA.
Stephen BuckleyLaboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Adrie H WestphalLaboratory of Biochemistry, Wageningen University, Wageningen, the Netherlands.
Simon LindhoudLaboratory of Biochemistry, Wageningen University, Wageningen, the Netherlands.
Sandrine GeorgeonLaboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Casper A GoverdeLaboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.ORCID 0009-0004-7409-4705
Georgios N HatzopoulosSwiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.ORCID 0000-0003-4382-4459
Pierre GönczySwiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.ORCID 0000-0002-6305-6883
Yannick D MullerDivision of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.ORCID 0000-0003-0513-7156
Gerald SchwankInstitute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.ORCID 0000-0003-0767-2953
Daan C SwartsLaboratory of Biochemistry, Wageningen University, Wageningen, the Netherlands.ORCID 0000-0003-4412-9191
Alex J VecchioDepartment of Structural Biology, University at Buffalo, Buffalo, NY, USA.ORCID 0000-0002-4222-7874
Bernard L SchneiderBertarelli Platform for Gene Therapy, Ecole Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland.ORCID 0000-0001-5485-8748
Sergey OvchinnikovMassachusetts Institute of Technology, Cambridge, MA, USA. so3@mit.edu.ORCID 0000-0003-2774-2744
Bruno E CorreiaLaboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland. bruno.correia@epfl.ch.ORCID 0000-0002-7377-8636
Funding
Structure and Assembly of Membrane Proteins at Tight JunctionsR35GM138368 · NIGMS · UNIVERSITY OF NEBRASKA LINCOLN · PI Alex J. Vecchio · 2020 to 2026
$3.1MExploring the unknown protein universe using evolutionary informationDP5OD026389 · OD · HARVARD UNIVERSITY · PI OVCHINNIKOV, SERGEY L. · 2018 to 2022
$2.0MNIGMS NIH HHS R35 GM138368NIH HHS DP5 OD026389
Abstract
Protein-protein interactions are at the core of all key biological processes. However, the complexity of the structural features that determine protein-protein interactions makes their design challenging. Here we present BindCraft, an open-source and automated pipeline for de novo protein binder design with experimental success rates of 10-100%. BindCraft leverages the weights of AlphaFold2 (ref.
Indexed as
Protein EngineeringProteinsAllergensAnimalsBinding SitesCRISPR-Associated Protein 9CRISPR-Cas SystemsGene EditingHumansImmunoglobulin EModels, MolecularProtein BindingReceptors, Cell SurfaceAllergensCRISPR-Associated Protein 9Immunoglobulin EProteinsReceptors, Cell Surface
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