ProteinMPNN

What is ProteinMPNN?

ProteinMPNN solves the inverse folding problem: given a protein backbone structure, what amino acid sequences will fold into that shape? This reverses the structure prediction question—instead of asking what structure a sequence adopts, it asks what sequences can adopt a given structure.

Developed at the Institute for Protein Design and published in Science (2022), ProteinMPNN achieves 52.4% native sequence recovery on test backbones, compared to 32.9% for the previous state-of-the-art Rosetta design software. Beyond accuracy, it runs in ~1 second per protein versus ~4 minutes for Rosetta.

Experimental validation has been extensive. Crystal structures and cryo-EM reconstructions confirm that designed sequences fold to their intended structures. The method has successfully rescued previously failed designs and enabled new applications from nanomaterials to target-binding proteins.

How does ProteinMPNN work?

ProteinMPNN represents protein structures as graphs where residues are nodes and edges connect spatially proximate residues (the 32–48 nearest Cα neighbors). The neural network learns from this geometric representation without requiring evolutionary information or sequence alignments.

Encoding structure

The encoder (3 layers, 128 hidden dimensions) processes pairwise distances between backbone atoms: N, Cα, C, O, and a virtual Cβ. These interatomic distances capture inter-residue geometry more effectively than dihedral angles or coordinate frames. Message passing between nodes and edges propagates structural information throughout the graph.

Decoding sequences

Rather than generating amino acids sequentially from N- to C-terminus, ProteinMPNN uses order-agnostic autoregressive decoding. During training, the model learns to predict amino acids in random order. At inference, each position is decoded conditioned on the structural encoding and any previously decoded positions.

This flexibility enables practical design scenarios: fixing certain residues while redesigning others, enforcing identical sequences across homo-oligomer chains, or biasing toward specific amino acid compositions.

How to use ProteinMPNN online

ProteinMPNN runs on ProteinIQ's GPU infrastructure, delivering sequence designs in seconds without local installation.

Inputs

Settings

Core settings

Temperature interpretation

Design constraints

Results

Each designed sequence includes:

Results can be exported as FASTA, CSV, or JSON, with backbone PDB files available in the Files tab.

Applications

Inverse folding enables several protein engineering workflows:

• De novo protein design: After generating a novel backbone with tools like RFdiffusion, ProteinMPNN provides sequences likely to fold into that structure
• Sequence optimization: Generate variants of existing proteins with potentially improved expression, solubility, or stability
• Functional homolog design: Create sequence-diverse proteins that maintain a target fold, useful when avoiding immune recognition or intellectual property constraints
• Rescue failed designs: Re-sequence backbones from computationally designed proteins that failed to express or fold

Limitations

ProteinMPNN designs sequences based solely on backbone geometry. It does not consider:

• Ligand interactions: For proteins with bound small molecules, metals, or nucleotides, use LigandMPNN instead
• Membrane environment: Standard ProteinMPNN was trained on soluble proteins. For transmembrane proteins or optimizing soluble expression, consider SolubleMPNN
• Stability optimization: While designs often fold well, ProteinMPNN does not explicitly optimize thermostability. Consider ThermoMPNN for stability predictions

Experimental validation remains essential—computational metrics predict but do not guarantee foldability or function.

Related tools

• LigandMPNN: Inverse folding with ligand, metal, and nucleotide context (63.3% recovery at binding sites)
• SolubleMPNN: ProteinMPNN variant trained exclusively on soluble proteins
• ESM-IF1: Alternative inverse folding method from Meta AI
• ThermoMPNN: Predict thermostability changes (ΔΔG) for mutations
• RFdiffusion: Generate novel protein backbones to sequence with ProteinMPNN