Ligand Constructor
General layout of Ligand Constructor program.
Three-dimensional ligand structure rendered in Balls and Sticks mode with a color scheme relevant to the partial charges.

An important part of construction of new medicinal agents and search for molecular targets is a design of three-dimensional molecule structures of new ligands of modification of existing structures. Visual, interactive design is often more convenient and speedy, and result is of higher quality. The Ligand Constructor program is a three-dimensional editor and enables creation of structures from both explicit atoms and groups in its database, which can be expanded by user if necessary. The program implements mouse-look navigation and supports both rotation around molecule and free flight mode, that is useful to inspect any molecule fragment. As opposed to other molecule constructors, Ligand Constructor operates on multiple bonds and can restore information about bond orders (including aromatic rings) from PDB files, traditionally containing no information of that kind. The program can also calculate values of atomic partial charges using an effective electronegativity equalization method, display a spatial structure of a ligand with colors encoding charge values, and generate a topology file of ligand molecule which is necessary for HBDock and BioPASED to work with. There is a selection expression interpreter with syntax similar to RasMol, and it allows to select certain molecules or parts of them. Molecule rendering is performed using hardware-accelerated OpenGL mode using some modern video card optimizations. Images generated by the program can be exported to one of several wide-spread graphic formats.

Ligand Constructor integrates with HBDock, in particular, it can save a structure of a ligand to the topology format understandable to docking calculation program. Besides there is a support for third-party plugins, both for supporting some other file formats and expanding the editor's functionality. The program supports Microsoft Windows operating system family (starting from Windows XP SP2) and Linux in X-windows mode, the language of its interface is English.

If you use the Ligand Constructor program in any work distributed or published, please include the following reference:

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