Benchling Releases AlphaFold beta Integration

By Bio-IT World Staff

May 19, 2022 | Benchling launched its AlphaFold beta feature today, designed to overcome challenges of implementation, computing power, and resourcing to make for ease of experimentation and integration with AlphaFold on the Benchling platform. 

AlphaFold is an artificial intelligence program developed by DeepMind that can predict the 3D structure of a protein from an amino acid sequence with unprecedented accuracy. Not only is it a scientific breakthrough with huge potential, but it is also emblematic of the new era of modern biotech: data-driven, open-sourced, collaborative and ultimately, faster than ever. 

But while AlphaFold is open source to use, Benchling believes setting up the machine learning architecture to run the AlphaFold algorithm is complicated, and takes significant engineering bandwidth to use in a stable, sustainable way.

Born out of a Benchling hackathon, the Benchling AlphaFold beta feature allows customers to select any amino acid sequence stored in Benchling, request a 3D structure for it, and visualize the results in its platform.  Customers can view and interact with the 3D structures in a Molstar (Mol*) viewer alongside the primary sequence. The structure files (.pdb format) also can be downloaded for more sophisticated modeling using third party applications. Scientists may readily share these protein structure files with other teammates, further extending the reach and utility of the data output.

Benchling’s AlphaFold beta will allow scientists to not only predict 3D structures of novel proteins directly within Benchling, but also centralize experimental context, collaborate with teammates, and connect with downstream scientific workflows on a single, secure platform.

“Our team gets excited about two things: science and bringing software to science,” said Ashu Singhal, president and co-founder of Benchling in a press release. “By making AlphaFold available to the biotech industry at the click of a button, scientists will be able to seamlessly experiment with this exciting advancement and find new ways to leverage AlphaFold output in their research. While the use cases for AlphaFold are still being explored and proven, Benchling’s goal with its beta feature is to support its community.”