arXiv:2512. 15133v3 Announce Type: replace-cross Abstract: Proteins inherently possess a consistent sequence-structure duality.
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arXiv:2609.37675v1 Announce Type: new Abstract: Protein Language Models (PLMs) have made remarkable progress following scaling laws established in natural language processing across sequence- and str...
ProtLingo is a protein language modeling framework that enhances a pretrained single‑sequence Transformer backbone with conditional local memory and sparse expert routing. It maps residue representations into discrete codes, composes local windows into latent N‑gram addresses, and retrieves reusable residual signals for recurring sequence contexts. The model also converts selected feed‑forward blocks into sparse Mixture‑of‑Experts layers, allowing residue‑dependent computation while activating only a subset of parameters, achieving competitive performance on protein fitness prediction, FLIP benchmarks, and supervised contact prediction with a 150M‑parameter backbone.
arXiv:2606. 02629v1 Announce Type: cross Abstract: Protein-protein interactions (PPIs) are essential for many biological processes.
SimpleDesign is a single-stage, end-to-end model for joint protein sequence and structure design that eliminates the need for multi-stage training. It combines discrete cross-entropy for sequences with a regression objective for structures, using a Mixture-of-Transformer architecture to handle modality-specific processing while maintaining global self-attention. Trained on over 2 million sequence-structure pairs, SimpleDesign achieves strong performance on co-design and unconditional generation benchmarks.
arXiv:2608. 12090v1 Announce Type: new Abstract: Protein language models (PLMs) have transferred the latest advances from natural language processing to computational biology.
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.