ArticlebioRxiv : the preprint server for biology2025
Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction.
Article in bioRxiv : the preprint server for biology, 2025. 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.
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- Development of Chimeric Ribonuclease A Inhibitor for Molecular Biology Applications: SUMO Fusion as an Engineering Strategy.Current issues in molecular biology · 2026Article
- Toward Rational Design of Imprinted Proteins Based on Albumins: Computational and Experimental Studies.Polymers · 2026Article
- Structure of the human P2X3 receptor reveals the basis for subtype-selective inhibition by sivopixant.PLoS biology · 2026Article
- Acoziborole resistance associated mutations in Trypanosoma brucei CPSF3.PLoS pathogens · 2026Article
- Functional Characterization of OasiCSP12: A Chemosensory Protein Regulating Olfaction and Phase Change inInsects · 2026Article
- Unlocking the undruggable spliceosome: generative AI and structural dynamics in cancer therapy.Frontiers in cell and developmental biology · 2026Review
- Beyond sequence similarity: toward function-based screening of nucleic acid synthesis.Frontiers in bioengineering and biotechnology · 2026Article
- Three hydrophobic surface binding a proteins link surface hydrophobicity to sporulation, biofilm formation, and host interaction inFrontiers in cellular and infection microbiology · 2026Article
- Molecular mechanism of ziresovir targeting the fusion glycoprotein of respiratory syncytial virus.PLoS pathogens · 2026Article
- NPC1 promotes HTNV replication by controlling innate immune response.Frontiers in immunology · 2026Article
- BAGEL: Protein engineering via exploration of an energy landscape.PLoS computational biology · 2025Article
- Systematic Exploration of Small-Molecule Binding via a Large Language Model Trained on Textualized Protein-Ligand Interactions.Molecules (Basel, Switzerland) · 2025Article
- Protein-Ligand Interactions: Recent Advances in Biophysics, Biochemistry, and Bioinformatics.International journal of molecular sciences · 2025Article
- Article
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
Accurately modeling biomolecular interactions is a central challenge in modern biology. While recent advances, such as AlphaFold3 and Boltz-1, have substantially improved our ability to predict biomolecular complex structures, these models still fall short in predicting binding affinity, a critical property underlying molecular function and therapeutic efficacy. Here, we present Boltz-2, a new structural biology foundation model that exhibits strong performance for both structure and affinity prediction. Boltz-2 introduces controllability features including experimental method conditioning, distance constraints, and multi-chain template integration for structure prediction, and is, to our knowledge, the first AI model to approach the performance of free-energy perturbation (FEP) methods in estimating small molecule-protein binding affinity. Crucially, it achieves strong correlation with experimental readouts on many benchmarks, while being at least 1000× more computationally efficient than FEP. By coupling Boltz-2 with a generative model for small molecules, we demonstrate an effective workflow to find diverse, synthesizable, high-affinity binders, as estimated by absolute FEP simulations on the TYK2 target. To foster broad adoption and further innovation at the intersection of machine learning and biology, we are releasing Boltz-2 weights, inference, and training code under a permissive open license, providing a robust and extensible foundation for both academic and industrial research.
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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.