arXiv:2608. 12192v1 Announce Type: new Abstract: Foundation models for protein structure prediction remain unreliable on certain targets.
By Aleksandra Kalisz, Jack Simons, Krisztina Sinkovics, Noam Ghenassia, Shikha Surana, Henry Moss, Paul Duckworth
arXiv:2607. 28437v1 Announce Type: new Abstract: Molecular optimization is commonly performed under a limited oracle budget, which makes deciding what to evaluate as important as deciding what to generate.
By Jiannan Yang, Veronika Thost, Xiang Ling, Tengfei Ma
arXiv:2606. 02386v1 Announce Type: new Abstract: Protein language models (PLMs) are passive oracles: they generate sequences in a single forward pass with no mechanism to consult external biophysical feedback or redirect generation when a candidate violates thermodynamic or structural constraints.
By Sahil Rahman, Maxx Richard Rahman
arXiv:2505. 20346v3 Announce Type: replace-cross Abstract: Function-guided protein design is a crucial task with significant applications in drug discovery and enzyme engineering.
By Jiahao Kuang, Nuowei Liu, Jie Wang, Changzhi Sun, Tao Ji, Yuanbin Wu
arXiv:2606. 31126v1 Announce Type: new Abstract: Predicting biomolecular properties from limited labeled data is a central bottleneck in protein engineering and small-molecule design.
By Davy Guan, Lu Zhang, Asiri Wijesinghe, Allen Zhu, He Zhao, Helen Power, F. Hafna Ahmed, Andrew Warden, Cheng Soon Ong, Daniel M. Steinberg
arXiv:2602.00663v3 Announce Type: replace
Abstract: Optimizing molecules to achieve desired properties is a central bottleneck across the chemical sciences, particularly in the pharmaceutical industr...
By Fabian P. Kr\"uger, Andrea Hunklinger, Adrian Wolny, Tim J. Adler, Igor Tetko, Santiago David Villalba