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Protein deimmunization framework that aligns a protein language model with GRPO to design sequences carrying fewer MHC Class I T-cell epitopes.
Multi-label classifier over ESM-2 embeddings that separates DNA-binding, RNA-binding, and dual-binding proteins using label-aware attention.
De novo protein backbone generation and sequence-conditioned folding using SE(3) flow matching over a physics-based, clash-free unfolding process.
De novo VHH nanobody binder design that conditions AlphaFold-Multimer with structural templates and language model sequence priors, no retraining.
Cross-species RBP-RNA binding site predictor that turns RNA-binding protein conservation into label smoothing, reaching 0.85 AUC from human to mouse.
Protein solubility mutation-effect predictor built on an anti-symmetric Siamese geometric graph network trained on deep mutational scanning data.
TCR-antigen binding prediction that adapts ESM-2 with LoRA on antigen-specific receptors and fuses the embeddings with a bipartite interaction graph.
Multimodal drug-target interaction model aligning SMILES, molecule text, taxonomy, and protein sequence with a Gramian volume contrastive objective.
Peptide aggregation predictor that scores amyloid propensity at single-residue resolution from ESM-2 embeddings, reaching 0.918 AUC on Serrano157.
Multimodal scientific foundation model unifying protein, DNA/RNA, and small-molecule structure in one token vocabulary for cross-domain reasoning.
SE(3)-equivariant chemical language model for pocket-based 3D molecule generation, used to design an HPK1 inhibitor with in vivo anti-tumor efficacy.
Protein-protein interaction predictor fusing evolutionary and structural embeddings to screen bacterial and host-pathogen proteomes in minutes.
De novo antibiotic design framework coupling a 6.4B-parameter protein language model with reinforcement learning to generate antimicrobial peptides.
Hierarchical transformer for virus discovery in metagenomes, classifying viral genomes across taxonomic ranks and flagging candidate novel lineages.
Protein structure prediction from general-purpose transformer blocks and flow matching, with no MSAs, pair representations, or triangle attention.
Antibody optimization by guided sequence-structure diffusion over antibody-antigen complexes, steered by affinity oracles trained on lab assay data.
Sequence-only protein-protein interaction prediction at proteome scale. Each protein is embedded once, so a pair score compares two stored vectors.
Protein language model that emulates molecular dynamics, generating equilibrium conformational ensembles and multi-timescale dynamic trajectories.
Transcription factor binding site prediction fusing DNA sequence with TF protein embeddings by cross-attention, generalizing zero-shot to unseen TFs.
Protein conformational ensemble and dynamics generator using latent diffusion to sample all-atom MD trajectories and transition pathways.
Generative antibody and nanobody design model that co-designs CDR sequences and antigen-bound structures for de novo design and affinity maturation.
Missense variant pathogenicity predictor that also ranks candidate diseases, aligning ESM-2 protein embeddings with PubMedBERT disease text.
Activation domain predictor scoring transcriptional activator strength from protein sequence, with a 20-model ensemble that reports uncertainty.