Molegro Virtual Docker 6.0.1

Bug fixes

• The ‘-nogui’ commandline option did not work when combined with the ‘-ps’ option.
• After installing Molegro Virtual Docker on Windows, the MVD shortcut on the desktop was linked to the MDM executable.
• Menu fonts in Molegro Data Modeller were unreadable on Windows XP.
• MVD crashed when docking using data sources and using MolDock SE.

Release date: June 13, 2013

Molegro Virtual Docker 6.0

Changes

• New and powerful regression features: Support Vector Machines regression and Partial Least Squares.
• Classification using either K-Nearest Neighbors or Support Vector Machine classification.
• Automated fine-tuning of regression and classification model parameters.
• Spring-Mass Maps for visualization of high-dimensional data.
• Clustering of data sets and subset selection.
• Principal Component Analysis.
• Outlier Detection.

Release date: November 7, 2012

Changes

• Energy Maps rendering provides volumetric visualization of protein force fields (see manual chapter 3.29).
• New options for multi-process docking. Multi-process docking may be invoked from the Docking Wizard, or using commandline options ‘-ps ‘ and ‘-gpus ‘ (see manual chapter 6.4).
• New Search Space Button (see manual chapter 3.8).
• Raytracer updates: now better reflects the OpenGL view.
• Added option for chain names in label dialog.
• Improved GPU error handling.
• Dock engine now checks for unique names during a single ‘DOCK’ operation.
• Optimization: The Batch Progress Dialog is now better at handling thousands of poses.
• Optimization: Displaceable water is now faster, when handling many displaceable water molecules.

Release date: December 2, 2011

New features

• This major release brings GPU-accelerated docking to Molegro Virtual Docker. This makes it possible to screen drug-like compounds up to 30 times faster than using conventional CPU-based methods.
• Support for GPU-accelerated docking on NVIDIA hardware with CUDA support (see Chapter 6 in User Manual for more details).
• New ‘Ligand Map’ feature available that provides an easy way to inspect and visualize protein-ligand interactions in 2D.

Release date: February 15, 2011

This release brings KNIME workflow support to Molegro Virtual Docker. This makes it possible to integrate MVD with existing workflows, such as accessing databases and preparing ligands using third-party software. After having upgraded MVD, please visit molegro.com/knime to install the KNIME plugins.

Changes

• Support for KNIME workflows.
• It is now possible to append MVDML workspaces to an existing workspace.
• MVDML is now the default docking format for saving poses.
• Molecule import now moves partial charges from hydrogens to the heavy atom they are attached to: since hydrogen bonds in MVD are handled by special terms in the scoring function, which does not take the hydrogen charge into account, moving the charge from hydrogens to heavy atoms ensures no charges are lost. Notice that MVD’s internal charge scheme does not assign charges to hydrogens, so this change is only relevant to molecules prepared by third party software.
• Protonation Wizard ‘repair’ function could in some cases corrupt protein structure: some (faulty) PDB files contains residues with multiple backbone atoms of same type (e.g. two atoms named ‘CA’ for the same residue). The Protein Wizard now detects these cases, and will not try to fix them (the Protein Wizard can only repair and mutate resides, where the backbone atoms can be uniquely identified).
• Better preparation of nitrogens in aromatic rings: for molecules without explicit hydrogens, MVD would sometimes wrongly protonate the nitrogens in aromatic rings.
• Linux build are now compiled on build machines (both 32 and 64 bit) using a newer version of the GCC compiler. The new build requires libstdc++.so.6.0.0 or later. Please contact us, if you run into problems with missing dependencies.