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: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:2606. 02629v1 Announce Type: cross Abstract: Protein-protein interactions (PPIs) are essential for many biological processes.
By Zaifei Yang, Samuel Ping-Man Choi, James Kwok
The paper introduces a method that uses orthogonal projection to remove the influence of known biochemical features from protein language model (PLM) embeddings, allowing the authors to assess how much these features contribute to protein fitness predictions. By applying this technique to high‑order and interaction effects, they demonstrate that eliminating these interpretable features reduces downstream classifier performance, indicating that PLM embeddings encode patterns correlated with biochemical properties. The authors also show that these biochemical features explain a substantial portion of the variance in the classifier’s predictions, suggesting that PLM embeddings capture biologically relevant information.
By Paulo Yanez Sarmiento, Pia Francesca Rissom, Manuel Pfeuffer, Marco Simnacher, Jordan F. Safer, Sumaiya Iqbal, Henrike O. Heyne, Nadja Klein, Bernhard Y. Renard
arXiv:2603.29529v2 Announce Type: replace-cross
Abstract: Using a statistical mechanics framework, we investigate the parameter space of transformer models trained on protein sequence data. We sample...
By L. Ghiringhelli, A. Zambon, G. Tiana
arXiv:2506. 13196v5 Announce Type: replace Abstract: Accurate prediction of protein-ligand binding affinity is critical for drug discovery.
By Han Liu, Keyan Ding, Peilin Chen, Yinwei Wei, Liqiang Nie, Dapeng Wu, Shiqi Wang