The Scaffold Tree - Visualization of the Scaffold Universe by Hierarchical Scaffold Classification

@article{citeulike:1063542, abstract = {Abstract: A hierarchical classification of chemical scaffolds (molecular framework, which is obtained by pruning all terminal side chains) has been introduced. The molecular frameworks form the leaf nodes in the hierarchy trees. By an iterative removal of rings, scaffolds forming the higher levels in the hierarchy tree are obtained. Prioritization rules ensure that less characteristic, peripheral rings are removed first. All scaffolds in the hierarchy tree are well-defined chemical entities making the classification chemically intuitive. The classification is deterministic, data-set-independent, and scales linearly with the number of compounds included in the data set. The application of the classification is demonstrated on two data sets extracted from the PubChem database, namely, pyruvate kinase binders and a collection of pesticides. The examples shown demonstrate that the classification procedure handles robustly synthetic structures and natural products.}, address = {Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland, and Max Planck Institute of Molecular Physiology and Fachbereich 3 - Chemical Biology, University of Dortmund, D-44227 Dortmund, Germany}, author = {Schuffenhauer, A. and Ertl, P. and Roggo, S. and Wetzel, S. and Koch, M. A. and Waldmann, H. }, citeulike-article-id = {1063542}, doi = {http://dx.doi.org/10.1021/ci600338x}, journal = {J. Chem. Inf. Model.}, keywords = {cheminformatics}, month = {January}, number = {1}, pages = {47--58}, posted-at = {2007-11-27 19:40:10}, priority = {0}, title = {The Scaffold Tree - Visualization of the Scaffold Universe by Hierarchical Scaffold Classification}, url = {http://dx.doi.org/10.1021/ci600338x}, volume = {47}, year = {2007} }

TY - JOUR ID - citeulike:1063542 L3 - citeulike-article-id:1063542 TI - The Scaffold Tree - Visualization of the Scaffold Universe by Hierarchical Scaffold Classification JF - J. Chem. Inf. Model. VL - 47 IS - 1 SP - 47 EP - 58 AD - Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland, and Max Planck Institute of Molecular Physiology and Fachbereich 3 - Chemical Biology, University of Dortmund, D-44227 Dortmund, Germany N2 - Abstract: A hierarchical classification of chemical scaffolds (molecular framework, which is obtained by pruning all terminal side chains) has been introduced. The molecular frameworks form the leaf nodes in the hierarchy trees. By an iterative removal of rings, scaffolds forming the higher levels in the hierarchy tree are obtained. Prioritization rules ensure that less characteristic, peripheral rings are removed first. All scaffolds in the hierarchy tree are well-defined chemical entities making the classification chemically intuitive. The classification is deterministic, data-set-independent, and scales linearly with the number of compounds included in the data set. The application of the classification is demonstrated on two data sets extracted from the PubChem database, namely, pyruvate kinase binders and a collection of pesticides. The examples shown demonstrate that the classification procedure handles robustly synthetic structures and natural products. KW - cheminformatics AU - Schuffenhauer, A AU - Ertl, P AU - Roggo, S AU - Wetzel, S AU - Koch, MA AU - Waldmann, H PY - 2007/01/22/ UR - http://dx.doi.org/10.1021/ci600338x ER -