Grok designs prostate cancer protein binders, Sonnet 5.5 makes the video
Grok used tools including BindCraft2 and RFdiffusion3 to generate over a thousand binder candidates and predict their structures, while the video was made with Claude Sonnet 5.5.
“Grok, design protein binders for prostate cancer research” In this binder design workflow test, Grok used various comp bio tools on neocloud resources to generate potential binder candidates against the AF-2 site of the androgen receptor (as many prostate cancers are AR driven). Grok created > 1K candidate sequences using BindCraft2, RFdiffusion3, and BoltzGen, along with ProteinMPNN sequence generation. ESMFold2-Fast and Boltz2 were used to predict the binder–target structures and evaluate their interfaces. A subset was also screened with ESMFold2-Full and Protenix to further assess binder–target placement. Next, to test a refolding workflow, new predictions of 30 candidate binder–target complexes were made via ESMFold2-Fast, ESMFold2-Full, Boltz2, and Protenix, where 5 random seeds were used per tool (another 600 predictions total). For a sequence diversification workflow, given starting predicted binder structures, new sequences were generated for 8 backbones using ProteinMPNN and the recent ProtonPotts, which takes into account protonation states. These seq gen tools created 64 redesign attempts. A subset of these was then evaluated with fresh structure predictions using ESMFold2-Fast, ESMFold2-Full, Boltz2, and Protenix. A pH-aware workflow continued with taking a subset of these, along with their parents, then using PDB2PQR / PROPKA and APBS to predict protonation states and calculate electrostatic contributions to the binder–target interactions, over a pH range of 6.5 -8.0. Ballpark compute costs ranged roughly ~1-26 cents per structure prediction or design attempt. The skill repo, BioSymphony Structure Factory, was used as a foundation for Grok to use these tools. Modal was used for the cloud resources. And, Claude Sonnet 5.5 made this video of the workflow test using ChimeraX, HyperFrames, and ElevenLabs.