proteinmpnn-nim

To design protein sequences for a specific 3D backbone, you can use inverse protein folding via the ProteinMPNN model. Provide a valid PDB file of the target backbone to generate compatible amino acid sequences.

Inverse protein folding generates stable amino acid sequences matching a fixed 3D protein backbone. It is needed when you have a novel backbone structure and want to produce candidate sequences for wet lab stability and binding affinity testing.

Yes, you can fix certain amino acid positions and exclude specific residues during protein design. The model supports complex design constraints including fixed positions, amino acid exclusions, and multi-chain redesign tasks.

Generate multiple candidate sequences from a PDB file by specifying the desired number of sequences and a sampling temperature. The tool outputs multi-FASTA files containing the sequences and associated confidence scores for downstream validation.

Yes, the ProteinMPNN model supports multi-chain protein complex redesign. You can apply chain-specific constraints and design constraints to generate sequences for complex multi-chain backbone structures.

You need a valid PDB file for your protein backbone input. You will receive multi-FASTA outputs containing the designed sequences along with associated confidence scores for downstream structural validation.