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BCL::MolAlign performs property-based small molecule alignment. Alignment is supported at three levels: (1) Rigid alignment - a single conformation of one molecule is aligned to a single conformation of another molecule; (2) Semi-flexible alignment - the conformation of one molecule is optimized to align to a single conformation of another molecule; and (3) Fully-flexible alignment - the conformations of two molecules are simultaneously optimized to align to one another. BCL::MolAlign accommodates ligand flexibility through a combination of pre-generated conformers from BCL::Conf and on-the-fly bond rotation. BCL::MolAlign converges on alignment poses by overlaying nearby substructures of the molecules through a multi-tiered Monte Carlo Metropolis sampling algorithm.
For this webserver, we use a non-proprietary rotamer library derived from the Crystallographic Open Database. Unpublished benchmarks showed that rotamers created using this rotamer library were of equivalent quality to the proprietary rotamer library used for the manuscript, which were derived from the Cambridge Structural Database.
If you use this webserve in your research, please cite: Brown BP, Mendenhall JL, Meiler J; "BCL::MolAlign: Three-Dimensional Small Molecule Alignment for
2 Pharmacophore Mapping", JCIM February 2019
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