rmgarnett/active_virtual_screening

MATLAB code to replicate experiments from https://doi.org/10.1007/s10822-015-9832-9

Active Virtual Screening

MATLAB code to replicate experiments from

Garnett, R., Gärtner, T. Vogt, M. and Bajorath, J.
Introducing the ‘active search’ method for iterative virtual screening.
Journal of Computer-Aided Molecular Design, 29(4):305–314.
DOI: 10.1007/s10822-015-9832-9

Dependencies

• Active learning toolbox
• Active search toolbox

Obtaining Data

Raw data can be downloaded as a compressed tar file here.

Preparing Data

You can precompute nearest neighbors with calculate_nearest_neighbors. You will need to compile the MEX file jaccard_nn.c first:

mex jaccard_nn.c

Running Experiments

You can replicate the active search experiments using run_experiments.