arXiv:2602. 06020v3 Announce Type: replace Abstract: How do protein structure prediction models fold proteins?
By Kevin Lu, Jannik Brinkmann, Stefan Huber, Aaron Mueller, Yonatan Belinkov, David Bau, Chris Wendler
arXiv:2607. 16087v1 Announce Type: new Abstract: AlphaFold2's 93 million parameters, shaped by the evolutionary record of protein structure encoded in the Protein Data Bank and in sequence alignments, are conventionally treated only as machinery for converting sequence to structure.
By Kaustav Mehta
arXiv:2512. 15133v3 Announce Type: replace-cross Abstract: Proteins inherently possess a consistent sequence-structure duality.
By Yi Zhou, Haohao Qu, Yunqing Liu, Shanru Lin, Le Song, Wenqi Fan
arXiv:2605. 01625v3 Announce Type: replace Abstract: Proteins are inherently multiscale physical systems whose functional properties emerge from coordinated structural organization across multiple spatial resolutions, ranging from atomic interactions to global fold topology.
By Viet Thanh Duy Nguyen, John K. Johnstone, Truong-Son Hy
arXiv:2607. 09998v1 Announce Type: new Abstract: Macrocyclic peptides are an increasingly important therapeutic modality, but existing computational methods for modeling their structures and properties are limited in scope and do not generalize well across the synthetically accessible chemical space.
By Vilya Research, :, Pascal Sturmfels, Milad Salem, Naozumi Hiranuma, Stephen Rettie, Xiaoliang Pan, Benjamin D. Sellers, Adam P. Moyer, Patrick J. Salveson, Ivan Anishchanka
arXiv:2607. 03787v1 Announce Type: new Abstract: Accurately modeling biomolecular interactions is a central bottleneck in biology and therapeutic discovery.
By Aureka AI OpenDDE project