https://www.nature.com/articles/s41589-025-02051-7 Mutant p53 protein accumulation is selectively targetable by proximity-inducing drugs Key figures [Supplementary Figure 1]: Establishes the clinical motivation by estimating that TP53-mutant cancers account for approximately 45.6% of…

https://pubs.acs.org/doi/10.1021/jacs.5c22222 Discovery of Covalent Ligands with AlphaFold3 Key figures [Figure 1]: Defines COValid as a covalent virtual-screening benchmark with acrylamide actives, property-matched decoys, and docking-parameter optimization. [Table 1]: Quantifies the…

https://www.pnas.org/doi/10.1073/pnas.2210435119 De novo mapping of α-helix recognition sites on protein surfaces using unbiased libraries Key figures Figure 1: Establishes that N,N′-(1,4-phenylene)bis(2-bromoacetamide) cysteine stapling increases α-helical structure across diverse 14-mer Helicons.…

https://www.nature.com/articles/s41467-023-42395-z Recognition and reprogramming of E3 ubiquitin ligase surfaces by α-helical peptides Key figures Figure 1: Defines the two-stage phage-display workflow that converts presenter-binding Helicons into focused trimerizer libraries and…

https://www.nature.com/articles/s41467-025-59940-7 Cyclic peptide structure prediction and design using AlphaFold2 Key figures [Figure 1]: Establishes that cyclic relative positional encoding enables AlphaFold2-based prediction of diverse native cyclic peptides, with 58/80 PDB…

https://www.nature.com/articles/s41589-025-01929-w Accurate de novo design of high-affinity protein-binding macrocycles using deep learning Key figures [Figure 1]: Defines RFpeptides as cyclic-offset RFdiffusion plus ProteinMPNN, AfCycDesign, and Rosetta, and validates that generated…

https://academic.oup.com/bib/article/26/5/bbaf488/8259888 Accurate structure prediction of cyclic peptides containing unnatural amino acids using HighFold3 Key figures Figure 1: Explains the Cyclization Switch that routes linear versus cyclic peptide inputs into AlphaFold…

https://www.nature.com/articles/s41598-025-20608-3 Structural determination of small proteins by cryo-EM using a coiled coil module strategy Key figures Figure 1: Explains the APH2 coiled-coil fusion design, including direct shared-helix fusion in CC2…

https://www.nature.com/articles/s41587-026-03081-9 Artificial allosteric protein switches with machine-learning-designed receptors Key figures Figure 1: Shows that circularly permuted natural and machine-learning-designed receptor domains can drive ligand-dependent activation of a β-lactamase reporter without…

https://www.science.org/doi/10.1126/science.adr7094 Deep learning–guided design of dynamic proteins Key figures Figure 1: Explains the full design workflow, from de novo generation of alternative states through deep learning–guided multistate design to mutation-based…