SpaceMACS

Overview

SpaceMACS is a novel search method for similarity-driven virtual screening in large combinatorial fragment spaces. SpaceMACS identifies maximum common connected induced substructures between a query and all products of a fragment space, e.g., a commercial make-on-demand library. SpaceMACS heavily exploits the fragment structure of those spaces. Therefore, users can screen billions or even trillions of compounds within seconds to minutes on standard computers. Its runtime depends on the number of results and the size of the fragment space representation. The runtime is commonly independent of the number of compounds represented. To explore fragment spaces, the SpaceMACS tool supports interactive command-line sessions and the processing of multiple queries, avoiding the need to load the space for every query separately.

Datasets

To search with SpaceMACS you can access the KnowledgeSpace at https://www.zbh.uni-hamburg.de/forschung/amd/datasets/knowledgespace.html.

Software Availability

SpaceMACS is freely available for non-commercial and academic users for Linux, macOS, and Windows as part of our NAOMI ChemBio Suite. To download SpaceMACS, register at https://software.zbh.uni-hamburg.de. Non-academic users can get an evaluation license free of charge. Only minimal setup steps are required to run SpaceMACS. All feedback (software.zbh(at)uni-hamburg.de) is highly appreciated.

References

Schmidt, R.; Klein, R.; Rarey, M. Maximum Common Substructure Searching in Combinatorial Make-on-Demand Compound Spaces. J Chem Inf Model 2022, 62 (9), 2133-2150. DOI: https://doi.org/10.1021/acs.jcim.1c00640