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Every biological foundation model, evaluated and ranked by the bio.rodeo team
Showing 649–672 of 1102 filtered models
Cross-domain molecular foundation model encoding small molecules, protein pockets, and their complexes in 2D and 3D on one Transformer backbone.
Full-atom flow matching model that generates a ligand and the induced-fit holo pocket together, starting from an apo binding site.
Protein structure embedding model that compresses each 3D fold into a single fixed-length vector for proteome-wide similarity search and clustering.
Dual-target protein sequence design conditioned on two receptor structures at once, combining a heterogeneous graph network with ESM-2 features.
Protein-conditional RNA design model that generates binding RNA sequences for any target protein, with no post-generation optimization step.
Promptable 3D segmentation for particle picking in cryo-electron tomography, conditioned on a reference subtomogram to detect any target complex.
Antibody language model pretrained on a curriculum that slides from unpaired to natively paired heavy/light sequences during masked-token training.
Generative design of protease substrates, producing 10-mer peptides conditioned on a target cleavage profile across 18 matrix metalloproteinases.
Structure-based 3D molecule generation that denoises a ligand at atom level and motif level at once, conditioned on the target protein's pocket.
Multimodal sequence model spanning proteins, coding DNA, and regulatory DNA for zero-shot fitness scoring and conditional sequence generation.
Bacterial protein-compound binding affinity prediction from amino acid sequence and SMILES, evaluated zero-shot on two species held out of training.
PROTAC degradation prediction from molecular graphs of the target, linker, and E3 ligase, combining cross-attention with contrastive learning.
Nanobody CDR design framework that alternates structure prediction, docking, and CDR generation in an expectation-maximization refinement loop.
Protein sequence design model that represents small molecules, nucleotides, and metals at atomic resolution, enabling ligand-aware enzyme design.
Protein design model generating novel Cas9 and Cas12 genome-editing enzymes by Bayesian search over a classifier-separated sequence latent space.
Prophage island detection in bacterial genomes and metagenome-assembled genomes, pairing a fine-tuned ESM-2 gene classifier with density clustering.
Protein structure tokenizer that encodes 3D backbones as discrete VQ-VAE tokens, fixing the codebook under-utilization that caps their vocabulary.
RNA sequence design model that generates protein-binding RNAs from a target structure alone, growing sequences outward from an anchored seed.
Protein conformational ensemble generator that denoises backbone geometry under language-model sequence conditioning with locality-aware attention.
Ternary complex structure predictor for PROTACs and molecular glues, placing E3 ligase, degrader, and target protein in one SE(3)-equivariant pass.
Graph deep learning framework fusing frozen protein language model embeddings with structure graphs to predict per-residue flexibility in antibodies.