DockingServer: GUI-based molecular docking on the web using Chemaxon tools
DockingServer (www.dockingserver.com) is an internet service developed by Virtua Drug Ltd that calculates the site, geometry and energy of small molecules interacting with proteins. It offers an easy and effective way for carrying out docking calculations, evaluating and presenting the results of docking calculations, writing method section for reports and organizes docking data.
DockingServer integrates the different tasks arising during the docking calculations by using third-party softwares for different steps. Molecular docking is based on Autodock software, electronic properties of the ligands are calculated with MOPAC and small molecule preparation and visualization are achieved using ChemAxon softwares.
The role of ChemAxon softwares in the DockingServer can be divided into three groups: 1. cxcalc calculations run in the background in order to i, calculate the protonation state of the ligands at a given pH; ii, to achieve rough geometry optimization of the ligands; iii, to calculate IUPAC names for the ligands; 2. file conversion tasks, like sdf conversion to multiple ligands, mol2 -> mol conversion etc. using molconvert command. 3. visualization and input of the ligands in 2D and 3D, visualization of the binding site-ligand interaction is achieved by using MarvinSketch and MarvinView.