v1.0.0 Released — Open Source (MIT)

PATCHR

Diffusion-based molecular structure inpainting

for Protein, RNA, DNA, and multi-chain complexes

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1.78 Å

Backbone RMSD

99.4%

Connectivity Pass

All-atom

Full Resolution

Download Patchr Studio Desktop

macOS (Apple Silicon)macOS (Intel)Windows Linux

Explore Features

Explore Patchr Atlas

Key Capabilities

Complete Molecular Inpainting Platform

PATCHR uses synchronized rigid template tracking and local refinement denoising to achieve state-of-the-art accuracy while preserving your experimental coordinates exactly as-is.

End-to-End Workflow

From PDB structure to completed model in Patchr Studio

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Structure Inpainting

Fill in missing residues and atoms using diffusion-based generative models with template conditioning.

Protein, DNA, RNA & Complexes

Works with proteins, nucleic acids, protein-ligand complexes, and multi-chain assemblies.

All-Atom Resolution

Generates complete all-atom structures, not just backbone traces. 1.78 Å Cα RMSD on benchmarks.

Simulation-Ready Output

Direct export to GROMACS, AMBER, and OpenMM for molecular dynamics simulations.

Dual Backend Support

Choose between Boltz-2 and Protenix backends. ~10s inference for 200-residue proteins.

CLI + Desktop GUI

Full command-line interface and Patchr Studio desktop app with Mol* 3D viewer integration.

Performance

Benchmark Results

Evaluated on 940 PDB40 structures with artificially introduced gaps mirroring real PDB missing-region statistics.

Method Comparison

RMSD (Å) on missing residues — lower is better

Method	Type	Cα RMSD	All-atom
PATCHR (full)	All-atom	1.78	2.54
Boltz-2 (unmodified)	All-atom	11.19	11.93
Boltz-2 + template + steering	All-atom	3.22	3.89
RFdiffusion2	All-atom	9.19	10.20
RFdiffusion	Backbone	2.04	—