Computational Drug Discovery

Molegro is a Danish company, developing novel high-quality drug discovery and data mining software, founded in 2005 by René Thomsen and Mikael Hvidtfeldt Christensen. In 2012, Molegro became part of CLC bio.

Molegro was formed based on research done by René Thomsen, PhD, who introduced a class of genetic algorithms – differential evolution – to the field of molecular docking. By mimicking the natural selection process, it became possible to solve problems more efficient and accurate than previous methods.

Since then, our solutions have been extended to cover new methods and new application areas, such as small molecule alignment and molecular descriptors. We combine methods from computational chemistry with novel methods from the field of machine learning, such as neural networks and support vector machines.

What does the name mean?

The name ‘Molegro’ is a combination of the words ‘Molecule’ and ‘Allegro’ (the musical term for quick or rapid tempo). The core of our business is high-performance drug discovery solutions leading to a faster drug-development process.

Read more about Molegro and get all the product details here.

Molecular Viewer

Molegro Molecular Viewer is a free cross-platform application for the visualization of molecules and Molegro Virtual Docker results.

Molegro Molecular Viewer is able to visualize most common molecular file formats (PDB, Mol2, SDF) as well as docking results from Molegro Virtual Docker.

Features at a glance

• Free!
• Cross-platform: Windows, Linux, and Mac OS X are supported
• Share and view results from Molegro Virtual Docker docking runs
• Imports and exports PDB, SDF, Mol2, and MVDML files
• Built-in raytracer for high-quality images
• Automatic preparation of molecules
• Molecular surface and backbone visualization
• Labels, sequence viewer and biomolecule generator
• Cropping of molecules and clipping planes
• Structural protein alignment
• Support for KNIME workflows

Downloads

The main user interface

Data Modeller

Molegro Data Modeller is a cross-platform application for Data Mining, Data Modelling, and Data Visualization.

The highly interactive user interface is ideal for fast and intuitive data exploration, contrary to complex workflow based solutions or command-driven statistical products.

Features at a glance

• Regression: Multiple Linear Regression, Partial Least Squares, Support Vector Machines, and Neural Networks
• Classification: K-Nearest-Neighbors and Support Vector Machines
• Chemistry: 2D depictions in spreadsheets and plots. SDF and SMILES support
• Feature selection and cross-validation is simple to set up and use (using built-in wizards)
• Automated fine-tuning of regression model parameters (using grid-based search)
• Principal Component Analysis (PCA)
• Visualization: Histograms, 2D scatter plots, 3D plots, and Spring-Mass Maps
• Clustering: K-means clustering and density-based clustering
• Built-in algebraic data transformation tool
• Outlier Detection
• Similarity Browser
• Correlation matrix dialog including descriptor pruning
• Sophisticated subset creation: create diverse subsets by sampling from n-dimensional grids
• Cross-platform: Windows, Linux, and Mac OS X are supported

Downloads

The main user interface

Virtual Grid

Molegro Virtual Grid creates an infrastructure for distributing docking runs on multiple machines.

By simply installing the MVG agent on a computer, its resources can be used transparently by the grid controller. Virtual Grid support is built into Molegro Virtual Docker: for instance, to dock a library of compounds against a receptor, simply setup a compound data source, and select ‘start job on Virtual Grid’ in the Docking Wizard.

Molegro Virtual Grid is multi-core aware and can be installed on any platform: Linux, Windows, and Mac. The machines in the grid do not need to run the same operating system.

Features at a glance

• Distribute MVD docking runs on multiple machines
• Simple management using the controller GUI
• Simple installation on any platform: Windows, Mac, and Linux. Machines on the grid do not need to run the same platform
• Automatic detection of running grid agents
• May run in the background on otherwise idle desktop machines
• Filter and reduce the results before analyzing them in MVD

Obtaining Molegro Virtual Grid

Molegro Virtual Grid is distributed together with Molegro Virtual Docker. If you have a licensed or trial version of Molegro Virtual Docker, you can use the basic version of Molegro Virtual Grid right away.

To obtain the extended license, please contact licenses@clcbio.com for a full featured trial-version.

To the left the MVG Controller interface shows the progress of a docking run. To the right the maximized MVG agent GUI is shown. The agent either runs as an icon in the task tray, in the maximized state, or without GUI.

Molegro Virtual Grid license types