Related tools
PocketFlow
PocketFlow is a structure-based molecular generative model that designs novel drug-like molecules within protein binding pockets. It uses autoregressive flow modeling with chemical knowledge to generate 100% chemically valid, highly drug-like compounds.
BoltzGen
BoltzGen is a state-of-the-art AI model for designing protein and peptide binders against any biomolecular target. Using generative diffusion models, it creates novel binders (proteins, peptides, nanobodies) with nanomolar-level binding affinity.
PepMimic
PepMimic designs short peptides that mimic the binding interface of a known protein binder on its target. From a reference protein complex, a latent diffusion model generates peptide candidates constrained to the target interface, and each candidate is scored by interface-mimicry against the reference binder.
GenMol
GenMol is a generative AI model from NVIDIA that creates novel drug-like molecules using masked discrete diffusion. It generates molecules in SAFE representation format and supports de novo generation, linker design, motif extension, and scaffold decoration.
PepMLM
Design linear peptide binders for target proteins using a target sequence-conditioned masked language model. PepMLM generates peptide sequences optimized to bind specific protein targets based on ESM-2 protein language modeling.
EvoDiff
EvoDiff is a diffusion-based protein sequence generation framework from Microsoft Research. ProteinIQ currently runs the EvoDiff-Seq OA_DM_38M model for unconditional protein generation, motif scaffolding, and user-sequence inpainting.
Genie 3
Generate protein structures and scaffolds with Genie 3, an all-atom SE(3)-equivariant diffusion model. Genie 3 supports unconditional protein generation, motif scaffolding, and hotspot-targeted binder design.
ODesign
All-atom generative AI for designing protein binders. Specify target binding sites and generate diverse binding proteins with fine-grained control over interaction parameters.
Proteo-R1
Reasoning-guided antibody CDR co-design for antibody-antigen complexes. Proteo-R1 identifies residue-level functional decisions and uses conditional diffusion to generate ranked designed structures with confidence metrics.
RFdiffusion
RFdiffusion is a state-of-the-art protein structure generation tool that uses diffusion models to design proteins de novo, create binders, scaffold motifs, and generate symmetric oligomers with atomic precision.