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| - CAESAR: A New Conformer Generation Algorithm Based on Recursive Buildup andLocal Rotational Symmetry Consideration
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| - A highly efficient conformer search algorithm based on a divide-and-conquer and recursive conformer build-up approach is presented in this paper. This approach is combined with consideration of local rotationalsymmetry so that conformer duplicates due to topological symmetry in the systematic search can be efficientlyeliminated. This new algorithm, termed CAESAR (Conformer Algorithm based on Energy Screening andRecursive Buildup), has been implemented in Discovery Studio 1.7 as part of the Catalyst ComponentCollection. CAESAR has been validated by comparing the conformer models generated by the new methodand Catalyst/FAST. CAESAR is consistently 5−20 times faster than Catalyst/FAST for all data setsinvestigated. The speedup is even more dramatic for molecules with high topological symmetry or formolecules that require a large number of conformers to be sampled. The quality of the conformer modelsgenerated by CAESAR has been validated by assessing the ability to reproduce the receptor-bound X-rayconformation of ligands extracted for the Protein Data Bank (PDB) and assessing the ability to adequatelycover the pharmacophore space. It is shown that CAESAR is able to reproduce the receptor-boundconformation slightly better than the Catalyst/FAST method for a data set of 918 ligands retrieved from thePDB. In addition, it is shown that CEASAR covers the pharmacophore space as well or better than Catalyst/FAST.
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