Frequently asked questions
How do I obtain a trial license?
To obtain a fully functional 30-day trial license for Molegro Virtual Docker, please see the instructions here.
To buy a license for Molegro Virtual Docker please see the sales contact page.
How do I cite Molegro Virtual Docker in publications and presentations?
Please use the following reference:
MolDock: A New Technique for High-Accuracy Molecular Docking
René Thomsen and Mikael H. Christensen
J. Med. Chem., 2006, 49(11), pp 3315 – 3321
Weblink: http://dx.doi.org/10.1021/jm051197e
How do I install a MVD license?
Copy the provided license file to the same folder as the executable file. Ensure that the license-file has the extension ‘.license’.
Which OS/platforms are supported?
MVD runs on Windows 7, Windows 8/8.1, Windows 10, Linux 64-bit (Ubuntu 16.04 and 18.04 are supported).
Can MVD handle DNA-Protein complexes?
It is possible to dock a ligand to a DNA-Protein complex. However, DNA molecules are currently parsed as ligands, so you have to convert them to ‘cofactors’ in order to take them into account during the docking simulation. Note that the scoring function used in MVD has only been calibrated and benchmarked on Protein-Ligand complexes.
Does MVD support metal ions in the binding site?
Metals ion are handled the same way as any other cofactor – steric (Van der Waals) and electrostatic interactions are taken into account. Currently we do not have special force field terms for metal coordination interactions.
Can MVD calculate the Binding Affinity?
The MolDock, MolDock grid, and the rerank score in MVD are not expressed in chemically relevant units. However, Molegro Virtual Docker can provide a rough estimate of the binding affinity. Please see the technology pages for more information.
Does MVD support flexible ligands and/or receptor flexibility?
The optimal position, rotation, and torsion angles of rotatable bonds are determined during the docking run. The rotatable bonds are single bond not part of a ring. Bonds can be chosen to be held fixed during docking (allowing for partial or fully rigid docking).
Ring conformations and bond lengths are not changed during the docking simulation. In order to investigate different ring conformations a molecular modeling tool should be used, and a few of the conformations with lowest energy should be docked.
It is possible to simulate ‘induced fit’ effects during the docking simulation: in MVD this is done by softening the potential during the docking (by increasing the tolerance of the PLP-potentials or by weakening selected sidechains interactions), docking a diverse set of poses, and finally optimizing the sidechain configurations. Notice that the backbone atoms of the protein will be held fixed – only the sidechain angles are changed.
How do I automate several dockings (batch jobs)?
Multiple ligands can be docked against the same target protein in the GUI. The docking wizard allows you to automatically save found poses during the docking simulation and to cluster and remove similar poses during the docking runs. MVD can also automatically prepare and dock multiple ligands from multi-molecule Mol2 or SDF-files (using the ‘Data Source’ importer).
It is possible to script and automate multiple docking runs from the console using the built-in scripting language or external scripting languages (such as Python).
Is MVD suitable for virtual screening?
It is possible to script the docking engine using the built-in scripting language or external scripting languages (such as Python). This makes it possible to distribute larger docking runs across several machines. Notice that the MVD license permits the user to install and run MVD on an unlimited number of machines or CPU’s.
How should ligands be prepared?
It is possible to prepare ligands in an external program. If the ligands are saved in a molecular data format capable of storing the various properties (such as charge and bond order), Molegro Virtual Docker will be able to read them.
However, it is not necessary to do so. Molegro Virtual Docker is able to determine atom connectivity, assign bond orders, hybridization, add explicit hydrogens, and assign charges automatically. It is also possible subsequently to modify the various properties in the GUI.
Molegro Virtual Docker can read ligands stored in the following formats:
- Protein Data Bank format (*.pdb *.ent)
- Sybyl Mol2 format (*.mol2)
- MDL Mol format (*.mol *.sdf *.sd *.mdl)
- Molegro MVDML format (*.mvdml)
How should proteins be prepared?
As with ligands, proteins can be prepared in an external program. However, it is not necessary to do so. Molegro Virtual Docker will perform a residue based template matching on the protein and assign the necessary molecular properties. Different protonation states can be set in the GUI using the Protonation Wizard.
Molegro Virtual Docker can read proteins stored in the following formats:
- Protein Data Bank format (*.pdb *.ent)
- Sybyl Mol2 format (*.mol2)
- Molegro MVDML format (*.mvdml)
Which file formats are supported?
Molegro Virtual Docker can read molecular structures stored in the following formats:
- Protein Data Bank format (*.pdb *.ent)
- Sybyl Mol2 format (*.mol2)
- MDL Mol format (*.mol *.sdf *.sd *.mdl)
- Molegro MVDML format (*.mvdml)
Can I modify the scoring function?
It is possible to rerank poses using a computationally more complex scoring function than the function used during docking. This reranking score function is a sum of several terms (such as Van der Waals forces, electrostatic interactions and solvent terms), which can be manually modified.
It is also possible to modify the energy landscape, by imposing constraints on the docking complex. This would allow you to either force certain interactions to occur (hard constraints) or to add a soft energy penalty (or reward) to certain regions of the complex.
Using Molegro Data Modeller it is also possible to build a custom model for predicting affinities. Prediction from custom models can be made directly in the Pose Organizer.
Does MVD support Protein-Protein docking?
No. MVD supports docking small molecules (ligands) to proteins only.