ROSHAMBO: Open-Source Molecular Alignment and 3D Similarity Scoring

Efficient virtual screening techniques are critical in drug discovery for identifying potential drug candidates. We present an open-source package for molecular alignment and 3D similarity calculations optimized for large-scale virtual screening of small molecules. This work parallels widely used proprietary tools and offers an approach complementary to structure-based virtual screening. Our package employs the PAPER software for optimizing molecular alignments based on Gaussian volume overlaps. GPU acceleration is utilized to significantly reduce computational time and resource requirements. After obtaining the optimal alignments between the target and the query molecules, both shape and color (based on pharmacophore features) scores are computed to assess molecular similarity, with aligned molecules optionally being output in sdf format. The package was benchmarked using the DUDE-Z public datasets. Results demonstrated the package's near-state-of-the-art performance and robustness across multiple target classes, with speed that enables many routine ligand-based drug discovery workflows. As an open-source and freely available resource (github.com/molecularinformatics/roshambo) with both a convenient Python API and command line interface, our package also addresses the need for accessible and efficient virtual screening tools in drug discovery.