Jens Sadowski

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Support vector machine (SVM) and artificial neural network (ANN) systems were applied to a drug/nondrug classification problem as an example of binary decision problems in early-phase virtual compound filtering and screening. The results indicate that solutions obtained by SVM training seem to be more robust with a smaller standard error compared to ANN(More)
Electronic properties located on the atoms of a molecule such as partial atomic charges as well as electronegativity and polarizability values are encoded by an autocorrelation vector accounting for the constitution of a molecule. This encoding procedure is able to distinguish between compounds being dopamine agonists and those being benzodiazepine receptor(More)
It is shown how a self-organizing neural network such as the one introduced by Kohonen can be used to analyze features of molecular surfaces, such as shape and the molecular electrostatic potential. On the one hand, two-dimensional maps of molecular surface properties can be generated and used for the comparison of a set of molecules. On the other hand, the(More)
Binary classification models able to discriminate between data sets of compounds are useful tools in a range of applications from compound acquisition to library design. In this paper we investigate the ability of artificial neural networks to discriminate between compound collections from various sources aiming at developing an "in-house likeness" scoring(More)
A hybrid approach for flexible 3D database searching is presented that addresses the problem of ring flexibility. It combines the explicit storage of up to 25 multiple conformations of rings, with up to eight atoms, generated by the 3D structure generator CORINA with the power of a torsional fitting technique implemented in the 3D database system UNITY. A(More)
A method has been developed which automatically generates SMARTS patterns for four-atomic torsional fragments, searches experimental structures in the Cambridge Crystallographic Database, and obtains rules for preferred torsion angles in drug-size molecules. These rules can be used for exhaustive conformational analysis using the popular conformer generator(More)
This work describes a data driven method for scaffold hopping by fragment replacement. A search database of scaffolds is created by cutting bonds of existing compounds in a combinatorial fashion. Three-dimensional structures of the scaffolds are then generated and made searchable based on the relative orientation of the broken bonds using an auxiliary index(More)
The software described in this document is furnished under a license and may be used and copied only in accordance with the terms of such license. CORINA is a registered trademark in the Federal Republic of Germany. Other product names and company names may be trademarks or registered trademarks of their respective owners, in the Federal Republic of Germany(More)