Web-Based Interface For Molecular Docking

Docking Server windows are organized into three modules following the basic steps of docking calculations:

(1) Protein set-up
(2) Ligand set-up
(3) Docking Calculation.

The user can create its own ligand, protein and dockings folder so that the ligands, proteins and dockings can be saved and organized for later use.

Protein set-up

The protein can be uploaded as a pdb file, or can directly be downloaded (after keyword search in the database if needed) from Protein Data Bank (www.rcsb.org). At this step the user can choose whether to include water molecules or any other heteroatoms present in the pdb file in the docking calculation. Add heteroatoms to my ligands command allows the adding of molecules present in the pdb files to the ligand folder. In the next step, the simulation box can be chosen. The simulation box can be either selected to cover only a known ligand binding site, or the whole target protein. Exact coordinates can be given as center of simula¬tion box similarly as in Autodock. In addition, Docking Server allows the user to define amino acids or heteroatoms present in the uploaded pdb file as center or borders of the simulation box.

Ligand set-up

The ligands can be uploaded or directly drawn. Besides single ligands, multiple ligands in sdf files can also be uploaded so that to enable high throughput docking of ligand libraries. The user can chose the desired pH affecting the protonation state of the ligand and whether semiempirical charges and optimization should be carried out during the process of ligand preparation.

Protein Ligand Docking

In the docking window the user can choose multiple ligands and/or dockings for the docking calculation. The docking calculation can be started using the default parameters; moreover, it is also possible to manually set docking parameters for more advanced users.

Finally, docking results are automatically processed in different ways to offer better understanding of the results:

1, resulting docking energies, frequencies and downloadable pdb coordinates are summarized in a table;
2, figures of the calculated ligand-protein complexes are automatically generated by VMD or can be manually rendered using the Jmol applet;
3, ligand-protein interaction tables are automatically generated that helps identify the driving forces of the complexation;
4, HB-plots (Bikadi, et al., 2007) are automatically generated to interpret the effects of the binding on the whole protein structure; 5, The applied methods and the according references are summarized.

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