Molecular Docking Server

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Analysis of the mode of interaction between ligands and their target proteins is of crucial significance in order to inspect different aspects of biochemical processes. Besides laboratory experiments, there is an emerging role of in-silico methods in investigating the interactions of ligands to proteins.

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How is Molecular Docking Server

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In-silico study of protein-ligand interaction involves molecular docking, where the binding energy and geometry of ligands, substrates or inherent drug candidates to target proteins is anticipated using computational chemistry methods.

The task in molecular docking assignments is to find the best ligand protein complex geometry. The problem is ordinarily seen as an optimization task where the goal is to minimize the intermolecular interaction energy between the two molecules of interest. Since the inherent estimate of ligand- protein complex geometry is ordinarily very large, different algorithms are used in order to accurately inspect the space of inherent conformations while decreasing the computational power needed for the docking calculation at the same time.

Thus, a molecular docking calculation consists of the following steps:

(1) Optimization of the ligand geometry, fancy pH-dependent partial charges, recognize rotatable bonds and

(2) fancy electrostatic properties of the protein of interest and define the ligand-binding region,

(3) The ligand-protein interaction is then calculated by a scoring function that includes terms and equations that reveal the intermolecular energies. The result of a docking calculation is a ligand-protein complex geometry and the corresponding binding energy. Therefore, for spoton interpretation of the results, a high-quality representation of the complex geometry is of great significance as well

(4)DockingServer integrates a estimate of computational chemistry software specifically aimed at correctly calculating parameters needed at different steps of the docking procedure, i.e. spoton ligand geometry optimization, energy minimization, fee calculation, docking calculation and protein-ligand complex representation.

Thus, the use of DockingServer allows the user to carry out very sufficient and robust docking calculation, which could not be achieved using singular software so far. Since the calculations run on our servers, the use of DockingServer does not wish excellent hardware or pre-installed software from the user.

The core of DockingServer web application is our integrating Php software connected to a MySql database, where the different tasks are automatically managed by daemons running on our servers and the input data will be read from the database and production data will be directed into the database.

The AutoGrid/AutoDock 4.0 (Morris, et al., 1998) agenda package is used for docking calculations, allowing docking of flexible ligands to proteins. With the help of Autodock agenda package the partial charges and atom types of the ligand and proteins can be assigned. However, the results of docking calculations strongly depend on the accuracy of charges calculated in the ligand.

Thus, Besides gift ligand partial fee calculation with the Auto-Dock agenda package DockingServer also integrates calculator plug-ins from Chemaxon (Csizmadia, 2000) and the Mopac2007 agenda (Stewart, 2007) for spoton pH-dependent protonation and ligand partial fee calculation. Moreover, geometry optimization, refinement of the ligand geometry using semiempirical methods (Pm6) can be carried out. self-acting conversions between essential file formats are achieved by Chemaxon tools.

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