Virtual Lab Data

Data for the Virtual Lab. Please see our paper The Virtual Lab: AI Agents Design New SARS-CoV-2 Nanobodies with Experimental Validation for more details.

The file ELISA_data_RBDs_nanobodies.xlsx contains the experimental ELISA binding data for the nanobodies designed by the Virtual Lab and several variants of SARS-CoV-2.

The file called "designed.zip" contains the computational results of running the nanobody design pipeline created by the Virtual Lab. This involves iterative rounds of running ESM, AlphaFold-Multimer, and Rosetta to identify mutations that optimize binding to the receptor binding domain (RBD) of the spike protein of the KP.3 variant of SARS-CoV-2. A summary of the contents is below.

round_0: This folder contains the ESM, AlphaFold-Multimer, and Rosetta results on the four starting wild-type nanobodies Ty1, Nb21, H11-D4, and VHH-72, which all bind to the Wuhan strain of SARS-CoV-2.

round_1, round_2, round_3, and round_4: These folders contain the ESM, AlphaFold-Multimer, and Rosetta results after iteratively introducing four mutations into the nanobodies.

selected: This folder contains the top mutant sequences across the four rounds.

combined: This folder contains the same top mutant sequences but with additional sequence tags for experimental validation.