Volker Hähnke

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We present a ligand-based virtual screening technique (PhAST) for rapid hit and lead structure searching in large compound databases. Molecules are represented as strings encoding the distribution of pharmacophoric features on the molecular graph. In contrast to other text-based methods using SMILES strings, we introduce a new form of text representation(More)
BACKGROUND Developing structure-activity relationships (SARs) of molecules is an important approach in facilitating hit exploration in the early stage of drug discovery. Although information on millions of compounds and their bioactivities is freely available to the public, it is very challenging to infer a meaningful and novel SAR from that information. (More)
Modulation of protein-protein interactions (PPI) has emerged as a new concept in rational drug design. Here, we present a computational protocol for identifying potential PPI inhibitors. Relevant regions of interfaces (epitopes) are predicted for three-dimensional protein models and serve as queries for virtual compound screening. We present a computational(More)
Previously, (Hähnke et al., J Comput Chem 2009, 30, 761) we presented the Pharmacophore Alignment Search Tool (PhAST), a ligand-based virtual screening technique representing molecules as strings coding pharmacophoric features and comparing them by global pairwise sequence alignment. To guarantee unambiguity during the reduction of two-dimensional molecular(More)
PubChem is an open repository for molecular structures, their properties and biological activities [1]. The number of deposited structures has been steadily increasing since its creation in 2004. Today, it contains more than 92 million substances (PubChem Substance) with 32 million unique small molecules (PubChem Compound). Consequently, visual inspection(More)
The text-based similarity searching method Pharmacophore Alignment Search Tool is grounded on pairwise comparisons of potential pharmacophoric points between a query and screening compounds. The underlying scoring matrix is of critical importance for successful virtual screening and hit retrieval from large compound libraries. Here, we compare three(More)
Previously, we proposed a ligand-based virtual screening technique (PhAST) based on global alignment of linearized interaction patterns. Here, we applied techniques developed for similarity assessment in local sequence alignments to our method resulting in p-values for chemical similarity. We compared two sampling strategies, a simple sampling strategy and(More)
BACKGROUND Atom environments and fragments find wide-spread use in chemical information and cheminformatics. They are the basis of prediction models, an integral part in similarity searching, and employed in structure search techniques. Most of these methods were developed and evaluated on the relatively small sets of chemical structures available at the(More)
The Pharmacophore Alignment Search Tool (PhAST) is a string-based approach to virtual screening. Molecules are represented by linear sequences which describe their respective pattern of interaction possibilities. The problem of molecule linearization is tackled by applying Minimum Volume Embedding in combination with a Diffusion Kernel to the molecular(More)