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A flexible approach to induced fit docking.
We present Fleksy, a new approach to consider both ligand and receptor flexibility in small molecule docking. Pivotal to our method is the use of a receptor ensemble to describe protein flexibility.Expand
Superposition of Three-Dimensional Chemical Structures Allowing for Conformational Flexibility by a Hybrid Method
The superposition method described here combines a genetic algorithm with a numerical optimization method. Expand
Pharmacophore Fingerprint-Based Approach to Binding Site Subpocket Similarity and Its Application to Bioisostere Replacement
We present KRIPO (Key Representation of Interaction in POckets): a new method for quantifying the similarities of binding site subpockets based on pharmacophore fingerprints of local binding sites together with their associated ligand fragments. Expand
Potential Drugs and Nondrugs: Prediction and Identification of Important Structural Features
Using decision trees, a model to discriminate between potential drugs and nondrugs has been developed. Expand
Structural Determinants for the Binding of Morphinan Agonists to the μ-Opioid Receptor
Atomistic descriptions of the μ-opioid receptor (μOR) noncovalently binding with two of its prototypical morphinan agonists, morphine (MOP) and hydromorphone (HMP), are investigated using molecularExpand
Locating Biologically Active Compounds in Medium-Sized Heterogeneous Datasets by Topological Autocorrelation Vectors: Dopamine and Benzodiazepine Agonists
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 the molecule. Expand
SyGMa: Combining Expert Knowledge and Empirical Scoring in the Prediction of Metabolites
Predictions of potential metabolites based on chemical structure are becoming increasingly important in drug discovery to guide medicinal chemistry efforts that address metabolic issues and toExpand
Evaluation of Molecular Surface Properties Using a Kohonen Neural Network
In this chapter the use of a Kohonen map in structure–activity relationship (SAR) and drug design is described. Expand