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MATLAB code to replicate experiments from https://doi.org/10.1007/s10822-015-9832-9
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README.md
calculate_nearest_neighbors.m
jaccard_nn.c
limited_search_bound_selector.m
run_experiments.m

README.md

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

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.

You can’t perform that action at this time.