GalaxyActDesign

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Method for GalaxyActDesign

GalaxyActDesign suggests mutations for affinity maturation from input protein-protein complex structure, based on a machine-learning-based scoring function derived from masked language model incorporating three-dimensional geometric features.

Inputs for GalaxyActDesign

The following information is required:

• Job name: Enter job name for your recognition.
• E-mail address: GalaxyWEB server will send progress reports of your job (if provided).

Input Protein Structure

You have to provide a protein complex structure in the PDB format.

Chain Assignment for Mutation

You have to provide chain IDs to be mutated. If you want to exclude specific chains from being considered, you can optionally provide them to the server. Both are comma-separated or concatenated list of PDB chain IDs (case insensitive).

Outputs for GalaxyActDesign

Suggested mutation list

Prefered scores for each mutation by GalaxyActDesign are provided as above figure. The first column identifies each mutation, combining {1-letter code of input amino acid}{chain ID}{residue number}{1-letter code of suggested amino acid}. The second column represents scores from the prediction. The higher the score, the stronger the predicted affinity.

Download

Suggested mutation list could be downloaded.