The paper proposes a new framework called ensemble-conditioned guidance that reframes molecular design as an optimisation over both the modes and properties of a molecule’s conformational ensemble. It allows 3D generative models to be conditioned simultaneously on multiple axes—such as shapes, pharmacophore profiles, or protein pockets—by adaptively combining vector fields from each condition. The authors introduce adaptive symmetry learning for composable conditions across reference frames, extend the framework to support flexible-size generation, and demonstrate its effectiveness on new benchmarks and practical drug‑discovery tasks, showing improved outcomes when conditioning on additional states compared to single‑state approaches.
By Ross Irwin, Alessandro Tibo, Jon Paul Janet, Simon Olsson
arXiv:2606. 14217v1 Announce Type: new Abstract: Accurate prediction of protein-ligand binding affinity is essential for structure-based drug discovery.
By Peng-Fei Sun, Chuan-Xian Ren, Hong Yan
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:2410.20317v2 Announce Type: replace
Abstract: Molecular dynamics (MD) simulations are a principled but computationally expensive approach for studying protein conformational variability, making...
By Siddharth Viswanath, Xingzhi Sun, Lucas Lee, Danqi Liao, Hiren Madhu, David R. Johnson, Jo\~ao Felipe Rocha, Egbert Castro, Jackson D. Grady, Michael Perlmutter, Dhananjay Bhaskar, Smita Krishnaswamy
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:2608.29207v1 Announce Type: new
Abstract: Protein structure modeling rests on a single computational primitive: the interaction between what a residue is (sequence content) and where it sits (t...
By Yifan Feng, Guanjie Cheng, Shihui Ying, Shaoyi Du, Yue Gao