Free to academics drug discovery tools foster innovations and independent research. Driven by that, BioSolveIT and the Center for Bioinformatics (ZBH) of the University of Hamburg have worked now for several years in close collaboration. Together, we develop cutting edge, free to academics technology for the benefit of molecular modelers everywhere, as well as medicinal chemists in the field of computer-aided molecular design.
This section of our web-page grants you early access to the latest achievements in the field. Some of these software programs are still at the prototype stage, but we still provide free access here*. We encourage you to try our tools, and let us know what you think.
We felt the need for a “step between” the outcome of a PhD thesis or other academic projects, and a completed product that commands a standard price-tag. We want to use this area to stimulate early adopters and gather feedback for our future product development by providing solid, free to academics tools.
PoseView is a free to academics tool that automatically generates publication-quality 2D structure-diagrams of protein-ligand complexes provided as 3D-input. Such input may come directly from crystal structures or be computed, for example, by a docking program. The interaction diagrams can be exported in various formats (PNG-, PDF- or XFIG files), with the latter providing the opportunity to modify the graphic in the full-featured graphics program XFIG.
The 2D depiction shows hydrogen bonds as dashed lines between the interaction partners on either side. Hydrophobic interactions are illustrated as smooth contour lines between the respective amino acids and the ligand. The ligand itself is drawn utilizing the 2Ddraw engine according to chemical drawing conventions. Various display options can be chosen, such as show/hide of interaction energies, show/hide hydrophobic contacts, as well as several labeling options.
PoseView may be used on the command-line for high-throughput processing of multiple data, or via an intuitive graphical user-interface, and is free of charge for academic research or evaluation purposes.
BioSolveIT is proud to contribute PoseView as a community service. The RCSB PDB uses PoseView to provide to its users 2D images of the macromolecule-ligand complexes on the Structure Summary page. PoseView is also available as a web service at poseview.zbh.uni-hamburg.de.
The PoseView user guide can be downloaded here.
K. Stierand, M. Rarey
Chem. Med. Chem., 2007, 2 (6), pp 853-869
Handling data sets of small molecules in various file formats is a “day to day” routine task. Frequently, users trust scripts or other “black-box” approaches. But what if you want more? Mona is an interactive, free to academics tool that can be used to prepare and visualize small-molecule datasets.
Mona has been built from the well-known Naomi cheminformatic network that has been proven to be robust, accurate and extremely efficient. Mona facilitates loading molecule files stored in SDF, MOL2 or SMILES-format. It scans entire directories for molecule data, and provides 2D depictions of hundreds of thousands of molecules. You can filter your data sets based on physical-chemical properties, functional groups, and substructures, as well as remove duplicates. Set-operations such as union, intersection, sub-set splitting are available. Mona visualizes property distribution of the compounds. You can even combine Mona with our SMARTS tools.
For the benefit of interactive use, Mona has been equipped with a database back-end that allows for extremely efficient handling. Upon import, numerous physic-chemical properties are calculated and deposited in the database. For a million molecules this may take half an hour. However, once stored, you may close and re-open the database within a matter minutes - gaining instant access to all properties and high-quality 2D depictions.
M. Hilbig, S. Urbaczek, I. Groth, S. Heuser, M. Rarey
J. Chem. Inf., 2013, 5:38 doi:10.1186/1758-2946-5-38
S. Urbaczek, A. Kolodzik, J.R. Fischer, T. Lippert, S. Heuser, T. Schulz-Gasch, M. Rarey
J. Chem. Inf. Model., 2011, 51 (12), pp 3199-3207
SMARTS is an extremely important concept for defining patterns in molecules. Unfortunately the SMARTS-language is quite complex and the description of a pattern easily becomes tricky and non-trivial. Here, BioSolveIT introduces two tools, developed by Karen Schomburg and Lars Wetzer at the Center for Bioinformatics at the University of Hamburg. These tools make life easier when working with SMARTS.
For example, see below a number of patterns illustrating the SMARTSviewer visualization concept, along with its dynamic legend, which describes each distinct atom and bond in natural language.
SMARTSeditor is an interactive GUI application that lets you draw substructure patterns. Jump-starting from a molecule, you may develop SMARTS in an intuitive fashion by editing topology and other properties. Using pre-defined patterns for common functional groups lets you quickly reach your goal. SMARTSeditor supports recursions, allowing you to reach any level of complexity without getting lost.
K. Schomburg, K. Wetzer, M. Rarey
Drug Discov Today, 2013 (13-14), pp 651-658
DoGSiteScorer is an automated pocket detection and analysis tool, which can be used for protein druggability assessment. Calculations are based on size, shape, and chemical features of automatically detected pockets. All these parameters are utilized in a support vector machine for druggability prediction. Advantages of DoGSiteScorer include excellent prediction rates on common benchmark sets, and unique sub-pocket calculations.
A. Volkamer, D. Kuhn, T. Grombacher, F. Rippmann, M. Rarey
J. Chem. Inf. Model. 2012, 52 (2), pp 360-372