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.
- 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- Linux build are now compiled on build machines (both 32 and 64 bit) using a newer version of the GCC compiler.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.