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.
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...
arXiv:2606. 02629v1 Announce Type: cross Abstract: Protein-protein interactions (PPIs) are essential for many biological processes.
arXiv:2604. 06336v2 Announce Type: replace-cross Abstract: Fragment-level representations provide a natural way to capture recurring molecular substructures and reuse their learned representations across molecules.
MT-ProtBERT is a multi‑task extension of ProtBERT designed for classifying intrinsically disordered proteins (IDPs) in low‑data settings. It combines Dynamic Window Masking, a Multi‑Scale 1D Convolutional classifier, and auxiliary biochemistry‑informed objectives to jointly optimize masked language modeling and domain‑specific tasks. In experiments on phosphorylation site prediction and protein compaction prediction, MT‑ProtBERT outperforms the RNN‑based IDP model PARROT across all limited‑data tasks.
arXiv:2607. 22777v1 Announce Type: cross Abstract: Protein language models learn transferable sequence representations.
arXiv:2608. 09099v1 Announce Type: new Abstract: Quantitative estimation of protein-ligand binding affinity from three-dimensional complex structures is a fundamental task in structure-based computational chemistry and molecular modeling.
CausalBind introduces a causal modeling framework for protein‑molecule virtual screening that focuses on sparse cross‑modality interactions rather than dense holistic alignment. By formalizing a V‑structure causal model with Heckman‑style selection, the authors prove that latent interaction concepts are identifiable only under sparsity constraints and propose three implementation variants. Experiments on DUD‑E and LIT‑PCBA benchmarks demonstrate that all variants outperform strong retrieval baselines, especially in early enrichment and out‑of‑distribution generalization.
arXiv:2608.21367v1 Announce Type: cross Abstract: Protein-peptide interactions are central to cellular regulation and peptide-based drug discovery, yet existing computational methods mainly focus on...
arXiv:2606. 27440v1 Announce Type: new Abstract: Foundation models for structural biology have achieved remarkable performance in predicting biomolecular structure and show promise for the design of proteins and small molecules.
arXiv:2608. 16094v1 Announce Type: new Abstract: Accurate protein structure prediction is fundamental to structural biology because protein structure underlies molecular function and provides a basis for mechanistic interpretation.
arXiv:2606. 14737v1 Announce Type: cross Abstract: Molecular dynamics (MD) simulations generate trajectories in a high-dimensional configuration space whose analysis critically depends on molecular descriptors, typically handcrafted observables or learned kinetic embeddings.