Academic Drug Discovery

Academic drug discovery is one of the keystones for independent research around the world. We at BioSolveIT develop cutting edge technology for the benefit of molecular modelers, as well as medicinal chemists in the field of computer-aided drug design. Our solutions are a perfect fit for small-molecule-oriented research groups at every step of the drug discovery and ligand optimization process.

Every group has individual requirements regarding the setup of their research environment. The scenarions can be as different as the challenge they tackle: a single medicinal chemist with expertise in molecular modeling, a whole group with focus on computational approaches for drug discovery, or introducing students to computational drug design.
Our solutions are tailored to address those needs with several usage scenarios.

BioSolveIT provides access to complementary computational drug discovery tools and programs. These raw diamonds may be used free of charge for academic research around the world or evaluation purposes.
If you are interested in a license, please let us know!*

• PoseView – 2D interaction diagrams
• Mona – small molecule handling
• SMARTSeditor - Define chemical patterns
• DoGSiteScorer – automated pocket detection and druggability assessment



* Important notice
No support is granted and any warranty or liability is hereby expressly excluded. Proceed at your own risk!
Please acknowledge scientific ownership. Any publication in reference to these downloads must cite the respective original publication.
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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.

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 Editor.

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.

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 SMARTSeditor. 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.

DoGSiteScorer is an automated pocket detection and analysis tool, which can be used for protein druggability assessment tailored for the early steps of academic drug discovery. 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.