Deep diversification of an AAV capsid protein by machine learning

Drew H. Bryant*, Ali Bashir*, Sam Sinai*, Nina K. Jain, Pierce J. Ogden, Patrick F. Riley, George M. Church^, Lucy J. Colwell^, Eric D. Kelsic^. Nature Biotechnology (2020).

Model and Dataset Analysis

Data for reproducing results:

• AAV2 capsid sequences (allseqs_20191230.csv.zip)

  • Capsid packaging assay results for 297k capsid sequences
  • Model training and validation datasets
  • Baseline additive and random datasets
  • Model-designed sequences
  • Model-selected sequences

• Subsampled model-designed sequence partitions (subsampled.tar.gz)

  • Used to normalize sequence subset sizes prior to clustering

• Clustering of all (viable + non-viable) model-designed sequences (clusters.tar.gz)

• Clustering of viable-only model-designed sequences (viable_clusters.tar.gz)

• Data with model scores associated with each sequence in the validation chip (ValidationChipwithModelScores.csv.bz2)

Additional information can be found here.