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Insight into steroid scaffold formation from the structure of human oxidosqualene cyclase
In higher organisms the formation of the steroid scaffold is catalysed exclusively by the membrane-bound oxidosqualene cyclase (OSC; lanosterol synthase). In a highly selective cyclization reactionExpand
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Validation and use of the MM-PBSA approach for drug discovery.
The MM-PBSA approach has become a popular method for calculating binding affinities of biomolecular complexes. Published application examples focus on small test sets and few proteins and, hence, areExpand
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TFD: Torsion Fingerprints As a New Measure To Compare Small Molecule Conformations
We have developed a novel measure to compare conformations of molecules called Torsion Fingerprints from a query molecule and generated conformations under consideration of acyclic bonds as well as ring systems. Expand
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Binding site characteristics in structure-based virtual screening: evaluation of current docking tools
Two new docking programs FRED (OpenEye Scientific Software) and Glide (Schrödinger, Inc.) in combination with various scoring functions implemented in these programs have been evaluated against a variety of seven protein targets (cyclooxygenase-2, estrogen receptor, p38 MAP kinase, gyrase B, thrombin, gelatinase A, neuraminidase) in order to assess their accuracy in virtual screening. Expand
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NAOMI: On the Almost Trivial Task of Reading Molecules from Different File formats
We present the chemical file format converter NAOMI, which provides efficient procedures for reliable handling of molecules from the common chemical file formats SDF, MOL2, and SMILES. Expand
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Recore: A Fast and Versatile Method for Scaffold Hopping Based on Small Molecule Crystal Structure Conformations
In this paper, a novel approach for scaffold replacement and a corresponding software tool, called Recore, is introduced. Expand
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Enzyme redesign: two mutations cooperate to convert cycloartenol synthase into an accurate lanosterol synthase.
Efforts to modify the catalytic specificity of enzymes consistently show that it is easier to broaden the substrate or product specificity of an accurate enzyme than to restrict the selectivity ofExpand
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Mechanistic insights into oxidosqualene cyclizations through homology modeling
We propose a structural model of 2,3‐oxidosqualene cyclases based on structural information of Alicyclobacillus acidocaldarius and propose a structure model of human OSC. Expand
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CONFECT: Conformations from an Expert Collection of Torsion Patterns
The generation of sets of low‐energy conformations for a given molecule is a central task in drug design. Herein we present a new conformation generator called CONFECT that builds on our previouslyExpand
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Isothermal titration calorimetry with micelles: Thermodynamics of inhibitor binding to carnitine palmitoyltransferase 2 membrane protein☆
Carnitine palmitoyl transferase 2 (CPT‐2) is a key enzyme in the mitochondrial fatty acid metabolism. The active site is comprised of a Y‐shaped tunnel with distinct binding sites for the substrateExpand
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