In addition to Althotas.com we are also the producers of DockingServer, an industry-leading online computational docking server. DockingServer has an active user base of more than 5000 users and has been cited in a number of peer-reviewed academic publications. Technology developed as part of DockingServer is also used here at Athotas.com as part of our core molecular docking experiments.
DockingServer provides a single access point to a number of leading, ‘gold-standard’ bioinformatics software packages commonly used in computational chemistry. Our default options allow users from all backgrounds to run appropriate experiments, while advanced configuration options are available for expert users. DockingServer can handle single protein-ligand docking experiments as well as high-throughput computational screens of multiple proteins and targets.
Because running an in silico docking experiment involves several steps from discrete software tools, whose results are required as input to subsequent steps, DockingServer uses a custom MySQL database to build a computational pipeline, automating this procedure. DockingServer makes use of AutoGrid/AutoDock 4, Chemaxon, and MOPAC2007 to carry out computations and inter-convert between file formats without user intervention being required. Results can be displayed using either Jmol or VMD and ligands can be inputted using Marvin Sketch or uploaded.
DockingVideo offers a web-based interface in order to create a video showing the process of complexation of a ligand to a protein as calculated by the docking software Autodock Vina.
DockingVideo calculates the preferred orientation of a ligand bound to a protein using molecular docking method. The process of the docking algorithm in finding the best complex geometry is then visualized.