The ap_prepare_inputs colab is provided as an aid to the users of the AlphaProteo Trusted Tester Program. It can be used to prototype requests and provides an interface to iterate on target protein regions, performing basic validation, and visualising the selected target.

To begin, please type or paste your target PDB ID into the corresponding field, then select "Runtime" -> "Run all" from the menu. See detailed instructions at the top of the colab.

The AlphaProteo model can be cited as follows:

@misc{zambaldi2024novodesignhighaffinityprotein,
  title         = {De novo design of high-affinity protein binders with AlphaProteo},
  author        = {Vinicius Zambaldi and David La and Alexander E. Chu and Harshnira Patani and Amy E. Danson and Tristan O. C. Kwan and Thomas Frerix and Rosalia G. Schneider and David Saxton and Ashok Thillaisundaram and Zachary Wu and Isabel Moraes and Oskar Lange and Eliseo Papa and Gabriella Stanton and Victor Martin and Sukhdeep Singh and Lai H. Wong and Russ Bates and Simon A. Kohl and Josh Abramson and Andrew W. Senior and Yilmaz Alguel and Mary Y. Wu and Irene M. Aspalter and Katie Bentley and David L. V. Bauer and Peter Cherepanov and Demis Hassabis and Pushmeet Kohli and Rob Fergus and Jue Wang},
  year          = {2024},
  eprint        = {2409.08022},
  archivePrefix = {arXiv},
  primaryClass  = {q-bio.BM},
  url           = {https://arxiv.org/abs/2409.08022},
}

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