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). ProteinsPlus has its focus on protein-ligand interactions. It supports (among others) the correct assignment of hydrogen atoms and tautomeric states, a first quality check via an automated electron density comparision, the detection and druggability estimation of binding sites and the fully automated construction of protein structure ensembles.
ProteinsPlus is described in more detail in a recent open-access publication in Nucleic Acid Research.
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 these expectations for certain classes. Naphthalene has to two rings, sure, but what about adamantane or cubane? What about macrocycles with para-substituted rings?
The existing solutions (SSSRs, RCs, RCPs) were either not unique (depend on the atom order) or not chemically meaningful in all cases. About five years ago, we presented the Unique Ring Families model (URFs) and showed that it is unique and chemically meaningful. Furthermore, we presented an efficient, polynomial-time algorithm for its computation. Unfortunately, this is very tough to implement. So we decided to develop an easy-to-use open source library for URF calculation. It is under New BSD license, so free to use and integrate for everybody. Hopefully, we were able to contribute in making cheminformatics software a little bit more unique in answering questions like 'Hey, to how many rings does this atom here belong?'.
More information ...
... for users: http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00292
... for developers: http://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00736
... for nerds: http://pubs.acs.org/doi/abs/10.1021/ci200629w
...on software: http://software.zbh.uni-hamburg.de
...about RingDecomposerLib: https://github.com/rareylab/RingDecomposerLib
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 on algorithms and database strategies to allow a flexible, efficient, and precise geometric access to protein-ligand interfaces. The method should neither be limited to keywords, precomputed interactions, chemical structures or predefined pharmacophoric points. It should be fast enough to really play with the data with no more than a decent laptop. Our studies resulted in a novel software piece named PELIKAN, an easy-to-use tool for all kinds of geometric searching in protein-ligand interfaces. No matter whether you are interested in ligand fragments with a specific binding motif, arrangements of side chain functional groups like aromatic cages, or specific interaction geometries like halogen-phenyl contacts. PELIKAN gives a precise answer, organizes and overlays all structures to the query. The whole story just appeared in JCIM http://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00561. The tool is part of our software suite which is freely available for academic use (see http://software.molecular-design.net). We preprocessed a series of databases containing protein-ligand complexes related to well-known datasets and interesting target families. More information on PELIKAN's web page (http://www.zbh.uni-hamburg.de/pelikan).
FSees is a novel software tool for contrained fragment space enumeration. A fragment space is a collection of fragments combined with specific linking rules. FSees creates a unified collection of molecules which can be created from a space within given physico-chemical property ranges. With FSees, we created the HELLS space, a collection of more than half a billion molecules created from drug-like molecular fragments (derived from DrugBank compounds). FSees is available as part of the AMD tools collection and can be downloaded from here. The HELLS space is also available for direct download
For further information see the FSees and HELLS webpages as well as the original publication http://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00117
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 definitions, calculation of interaction fingerprints, or superimposition of protein binding sites. In contrast to most other alignment techniques, ASCONA focuses on an accurate alignment of sequentially similar, but structurally highly deviating binding sites.
ASCONA is available as part of the AMD tools bundle from here. Furthermore, it is part of our protein binding site extraction pipeline with the ProteinsPlus web service.
For further information please see pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00210
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 implementiert einzelne Moleküle zu vergleichen: Durch die 2D Ausrichtung von Strukturdiagrammen lassen sich die Gemeinsamkeiten einzelner Moleküle einfach vergleichen. Jetzt hier herunterladen!
The SMARTSminer automatically generates discriminative patterns. Starting from two sets of molecules, one set containing molecules a pattern shall match and a second set containing patterns which shall not match, the algorithm searches for a sugraph with SMARTS functionalities. Integrated into the SMARTSeditor, these patterns are visualized and easily can be further modified and studied. The SMARTSeditor including the new SMARTSminer functionality can be downloaded from here.
Bietz, S. Schomburg, K. T. Hilbig, M. Rarey, M. (2015). Discriminative Chemical Patterns: Automatic and Interactive Design. Journal of Chemical Information and Modeling, in press.