This work established a robust framework for identifying and prioritizing high-confidence DARPin candidates for experimental validation, and identified mesothelin-targeting DARPin candidates with predicted structural confidences approaching those of a structurally validated picomolar-affinity binder.
These results establish motif scaffolding of surface-complementing seeds as an effective strategy for overcoming current limitations of de novo generative models, enabling the design of proteins that can engage challenging interface sites.
D. Britton, Dia A. Ghose, J. Halpin et al.· bioRxiv· 0 citations
Biomolecular binder design for peptides and antibodies requires generating diverse candidates that satisfy stringent three-dimensional geometric constraints while enabling affinity-oriented exploration under strong structural priors. In current generative models, the effective search space for structurally feasible bin...
Zhihua Tian, Jia-Le Zhou, Ru-Bo Wang et al.· Proceedings of the 32nd ACM...· 0 citations
Current structure-based drug design generative models often struggle to faithfully recapitulate genuine ligand-protein binding interactions. Instead, under the coupling of implicit learning architectures and biased training data, they tend to learn spurious statistical correlations. To address this, we propose EIP-Diff...
Huabin Du, Mingyang Wang, M. Luo et al.· Journal of the American Chem...· 0 citations
HEDGEHOG is introduced, a unified six-stage filtration benchmark that is inspired by industrial hit identification workflows and exposes a central limitation of current molecular generators: molecules that appear acceptable under isolated criteria rarely satisfy medicinal chemistry, synthesis, docking, and 3D pose filt...
Daria A. Ryabchenko, Pavel Gurevich, S. Kadyrov et al.· arXiv.org· 0 citations
HighPlay2 is presented as a feasible framework for the early-stage design and screening of cyclic peptide candidates containing ncAAs, while further affinity maturation and experimental structural validation remain necessary.
Huitian Lin, Wentong Wang, Ning Zhu et al.· European journal of medicina...· 0 citations
A clear pattern is revealed in LLM spatial capabilities: while they still lag behind state-of-the-art approaches, they are promising and can handle multiple spatial constraints simultaneously, enabling scaling to heterogeneous setups.
Thomas MacDougall, Maksim Kuznetsov, Roman Schutski et al.· arXiv.org· 1 citation
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