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RFdiffusion All-Atom (RFdiffusionAA)

By Institute for Protein Design (Baker Lab) →

All-atom diffusion modeling for proteins, small molecules, and nucleic acids

RFdiffusion All-Atom extends the groundbreaking RFdiffusion framework to model and generate proteins in the explicit context of non-protein atoms, including small-molecule ligands, metal ions, and nucleic acids.

De novo design of protein binding pockets around specified small moleculesCo-generation of protein binders with coordinated catalytic ions and cofactorsFull atomic coordinate representation during the reverse diffusion trajectorySeamless integration with LigandMPNN for sequence design
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Overview

RFdiffusion All-Atom extends the groundbreaking RFdiffusion framework to model and generate proteins in the explicit context of non-protein atoms, including small-molecule ligands, metal ions, and nucleic acids.

Information checked against an official source; not a hands-on test. Source · Last reviewed: 20/09/2026, 11:09:40

Key Features

  • De novo design of protein binding pockets around specified small molecules
  • Co-generation of protein binders with coordinated catalytic ions and cofactors
  • Full atomic coordinate representation during the reverse diffusion trajectory
  • Seamless integration with LigandMPNN for sequence design
Interactive 3D Structure

RFdiffusion All-Atom (RFdiffusionAA) Predicted Complex

Streams real 3D atomic coordinates from RCSB Protein Data Bank
⇄ Drag to rotate · Scroll to zoom
pLDDT / B-Factor:
>90 Very high 70-90 Confident 50-70 Low <50 Very low

Academic Context & Research Evidence

Biological & Workflow Fit

Biological Application
Enzyme active site design, small molecule sensor engineering, and drug receptor design
Research Workflow
Diffusion of protein backbone and sidechains around explicit ligand coordinates
Compute & Hardware
1x NVIDIA A100 or RTX 4090 GPU (>= 24GB VRAM)
Licensing & Academic Use
Open Source for academic research; commercial license required for for-profit use
Documented Evidence
View validation publication / source ↗

Cite this Tool

Use this citation format when referencing RFdiffusion All-Atom (RFdiffusionAA) in scientific publications and benchmark papers.

@software{rfdiffusion_all_atom_2026,
  title = {{RFdiffusion All-Atom (RFdiffusionAA)}},
  author = {{Institute for Protein Design (Baker Lab)}},
  year = {2026},
  url = {https://github.com/baker-laboratory/rf_diffusion_all_atom},
  note = {Indexed on aibioatlas - AI for Biology and Drug Discovery}
}

Peer-Reviewed Literature & Preprints

Live scientific citations streamed from Europe PMC and PubMed for RFdiffusion All-Atom (RFdiffusionAA).

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Technical / Product Information

Missing values mean the catalog has no recorded information. They do not mean a feature is absent.

Entry typeAI Model / Software
Access modeAcademic Open Source
AI roleDe Novo Molecular Diffusion
Input dataNot recorded
Output dataNot recorded
Licence conditionsOpen Source for academic research; commercial license required for for-profit use
Commercial eligibilityCommercial licensing available through University of Washington CoMotion
Compute requirements1x NVIDIA A100 or RTX 4090 GPU (>= 24GB VRAM)
ValidationNot recorded
TypeGenerative all-atom diffusion model
Intended useNot recorded
CompatibilityNot recorded
ManufacturerInstitute for Protein Design
Biological applicationEnzyme active site design, small molecule sensor engineering, and drug receptor design
Research workflowDiffusion of protein backbone and sidechains around explicit ligand coordinates
Evidence levelPeer-reviewed research (Science 2024)
Integration evidencehttps://github.com/baker-laboratory/rf_diffusion_all_atom
Laboratory handoffDesigns validated via yeast surface display and biolayer interferometry (BLI)
AvailabilityAvailable on GitHub
Price / accessFree for academic research / Paid commercial license

Research fit & compatibility

No software–hardware integration has been verified for this entry yet. Explore documented research workflows.

Gallery & resources

No licensed product photograph recorded for RFdiffusion All-Atom (RFdiffusionAA) yet. Visit the official resource below for manufacturer imagery.

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FAQ

Where is this product available?

Available on GitHub

How is pricing handled?

Prices reflect the source at its last check. Confirm current pricing and regional availability on the official site.

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Peer Reviews & Community Ratings

Feedback from researchers and computational biologists evaluating RFdiffusion All-Atom (RFdiffusionAA).

5.0
★★★★★Based on 0 researcher evaluations
Biological Accuracy
4.8/5
Ease of Installation
4.3/5
Documentation & Code
4.6/5