Nils-Ole Friedrich, Méliné Simsir and Johannes Kirchmair from the Junior Research Group for Applied Cheminformatics and Molecular Design have conducted a comprehensive study of protein-bound conformations of drugs and drug-like molecules.
Using an elaborate cheminformatics pipeline, which also...
Prof. Kirchmair has been appointed Visiting Professor at the University of Vienna, Department of Pharmacy. In the summer semester of 2018 he will be giving lectures in pharmacoinformatics and medicinal chemistry.
False-positive assay signals triggered by badly behaving compounds continue to pose a major challenge to experimental screening. A free web service developed by scientists of the Kirchmair lab, called Hit Dexter, is able to identify such compounds with high accuracy, enabling chemists to make...
Three-dimensional approaches in computer-aided molecular design such as ligand docking, pharmacophore modeling and 3D QSAR rely on the accurate representation of the protein- bound conformations of small molecules. A common approach to covering the conformational space is to compute ensembles...
X-ray crystallography is the backbone of modern, structure-based molecular drug design. While protein structures are easily accessible via the PDB and frequently used, it is to our experience not common practice to inspect the original experimental data, the electron density. Typically, only...
A recently published article by Ya Chen, Christina de Bruyn Kops and Johannes Kirchmair reviews 25 virtual and 31 physical natural product libraries that are useful for applications in cheminformatics, in particular virtual screening. The overview includes detailed information about each...
ProteinsPlus is a web service established at the ZBH in 2016 and now part of denbi - the German Network for Bioinformatics Infrastructure. The web server is the first of its kind supporting early preprocessing and selection steps for protein structures from the Protein Data Bank (PDB)...
This publication reports on the development of new in silico models for the prediction of metabolically labile atom positions ("sites of metabolism") in small molecules. The ability to predict and identify these atom positions can aid in the derivation of likely metabolites and, consequently...
In this publication, an extensive evaluation of hydrogen bond interaction geometries within protein-ligand complexes is presented. Based on the vast amount of protein structures nowadays available in the Brookhaven Protein Data Bank, interaction preferences were analyzed for 21 functional...
In this publication, mutational effects in protein complexes are predicted using the HYDE scoring function. Additionally, an extensive evaluation procedure - remutation, cross-mutations, and protein stability predictions - is presented including a freely available data set to perform these...
Proteinochromismus bezeichnet den Einfluss des Proteingerüst auf die Lichtabsorption durch Liganden und aktive Zentren. Diese Prozesse spielen eine wichtige Rolle etwa für die Photosynthese oder für so wichtige biomolekulare Werkzeuge wie das GFP. Um die Vorgänge richtig zu verstehen, benötigt...
During his PhD Stefan developed a series of tools enabling the automated generation of large protein structure ensembles including fast structure searching, binding site focused alignment, protonation, and conformer selection. The whole workflow, named SIENA (http://pubs.acs.org/doi/abs/10.1021...
This article by Stefan Bietz and Matthias Rarey introduces ASCONA, a new software for the detection and the alignment of active site conformations.
ASCONA generates residue-wise mapping of active site residues that can, e.g., be used for flexibility analysis, transfer of binding site...
mRAISE is a tool for ligand-based virtual screening based on the RAISE (=RApid Index-based Screening Engine) technology. The triangle-descriptor abstraction of small molecules allows fast non-sequential screening of millions of compounds. Calculated alignments are scored using a Gaussian-type...
Molekülen in Sets können nun beliebige Eigenschaften aus SD Dateien zugeordnet werden. Ein neues clustering erlaubt es Moleküle nach diesen Eigenschaften oder nach Ähnlichkeit zu clustern. In der Cluster Anzeige werden die einzelnen cluster dargestellt. Außerdem wurde eine neue Möglichkeit...
In dieser Veröffentlichung aus den Arbeitskreisen Kirchmair und Rarey wird ein neues Verfahren zur vollautomatischen Extraktion hoch-qualitativer Strukturdaten von proteingebundenen Liganden aus der Protein Datenbank (PDB) vorgestellt. Bisher konnten solche Daten nur durch mühsame und...
In dieser Veröffentlichung aus dem Arbeitskreis Kirchmair wird die computergeleitete Identifizierung und Charakterisierung einer neuen Substanzklasse beschrieben, welche sowohl virale als auch bakterielle Neuraminidasen hemmt. Neuraminidasen sind etablierte Zielproteine für die Prävention und...
Neues Paper: Evaluation of DFT-D3 dispersion corrections for various structural benchmark sets
In dieser Veröffentlichung wird die Erweiterung der im Arbeitskreis Schwabe entwickelte DFT-D3(CSO)-Dispersionskorrektur für die Optimierung von Molekülstrukturen vorgestellt und evaluiert. Des...
We have more than 120,000 protein structures at our fingertips, we are able to quickly access this data by all kind of keyword and sequence queries. But when it comes to querying the real content, the 3D structure, our computational methods are rather limited. Over the past four years we worked...
One of the very fundamental problems in cheminformatics is the decomposition of complex ringsystems into sets of rings. While chemists usually have a very clear picture in mind of what rings a molecule consists, the classical algorithms for ring decomposition had their difficulties in matching...
