| Efficient Clustering of Molecular Conformations (2007) | |||||||||||||||
Abstract | |||||||||||||||
| ) B. COOK L. E. KAVRAKI R. MOTWANI y During the process of pharmaceutical drug design, computational chemists often compute different lowenergy conformations of small drug molecules (ligands). Such conformations are used in solving docking problems [5] and in pharmacophore identification [3]. Most methods that identify different low-energy conformations of ligands employ clustering to partition the generated conformations (typically tens of thousands) into sets that capture geometric similarity. Since the generation and clustering of conformations is a time-consuming operation [2], recent work focuses on devising faster algorithms for these problems. In this paper, we consider the problem of clustering conformations of ligands with 3-20 rotatable bonds. We report a number of experiments which indicate that while clustering based on distance measures defined over the workspace (W-space) has much better quality than clustering based on distance measures defined over the conformati... | |||||||||||||||
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