Dear Reader,

In this newsletter you can read about the latest release of Molegro Virtual Docker, version 3.0 (released September 25th, 2008). This major update introduced several new features:

Molecular descriptors. Molegro Virtual Docker is now able to calculate various molecular descriptors, including our own topological CFDM (Chemical Feature Distance Matrix) descriptors and a number of standard descriptors (like molecular weight and hydrogen donor count).

Molecular descriptors are useful for a number of purposes - for instance it is possible to build regression models for predicting properties like toxicity or drug likeness in either the Data Analyzer or the Molegro Data Modeller. Molecular Descriptors can also be used for clustering or subset creation.

The new built-in Similarity Browser in the Data Analyzer makes it possible to screen a set of compounds for similarity with for instance a known binder. The current descriptors in MVD are topological, which means they are not dependent on the actual conformation of the molecule.

Displaced water model. When docking with explicit water molecules, the new displaced water model allows a ligand to displace individual water molecules, making it possible to more accurately model water mediated ligand binding.

Protein preparation and mutation. The old protonation wizard has been replaced by a new Protein Preparation dialog. It is now easy to quickly validate a target receptor and to inspect and change protonation states. It is also possible to repair, mutate, and minimize side chains.

If you haven't done it already, be sure to download the latest version of Molegro Virtual Docker (requires login).

Major Molegro Data Modeller release coming up

The next release of Molegro Data Modeller will include 2D molecule depiction - a feature that a lot of users have requested. We are adding SMILES parsing and SDF import and will integrate molecule depiction several places in MDM including the spreadsheet and the plotting dialogs.

These, and several other new features will be part of Molegro Data Modeller version 2.0, which will be released at the end of this year.

Help us improve our products

We are always interested in feedback. If you do have something you would like to see integrated in one of our products, please email me: mhc@molego.com

Best regards,
Mikael Hvidtfeldt Christensen,
Head of Development,
Molegro.

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