DockingServer Frequently Asked Questions
- What is Dockingserver good for?
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Molecular docking is a method which predicts the preferred orientation of one molecule (ligand) to a second (protein) when forming a stable complex. Moreover, knowledge of the preferred orientation may be used to calculate the binding affinity between two molecules (e.g. free enthalpy of binding).
With the aim of DockingServer, you do not need to be a computer expert to produce high-quality molecular modeling results. DockingServer does the most difficult parts of the molecular modeling job automatically: it calculates the geometry and electronic properties of the ligands at a given pH, prepares the protein structure to a dock-ready form, runs the calculations, and analyzes the results. Dockingserver can automatically handle multi-ligand files and process thousands of ligands with just a few clicks. Similarly, thousands of docking runs can be done with a few steps to identify the most effective small molecules for given targets.
- Where can I get molecule coordinate files?
- In addition to the public proteins and ligands that are distributed with DockingServer, the major source of data files is the Protein Data Bank at Brookhaven National Labs. This is the main repository for all of the world"s known 3D crystallography and nuclear magnetic resonance (NMR) structures of proteins and nucleic acids. You can download these structures within the DockingServer. Small molecule coordinates are not necessary for Dockingserver, because they can be computed form 2D structures. There are many databases if you need input structures for your ligands, e.g. the ZINC database.
- How can I create the PDB file for a particular sequence?
- If you are interested in a protein, which experimental structure has not been determined yet, its structure should be modeled first. There are several ways to do that: i, You can try homology modeling programs, like Modeller (www.salilab.org/modeller) ii, you might consider using homology modeling servers, e.g. the Swiss-Model server that performs comparative homology molecular modeling to return the potential 3D structure to you as a PDB file iii, or you can contact our experienced team at info@virtuadrug.com to produce high-quality models for your research.
- How do I create high resolution images in DockingServer?
- High-quality images of dockings are automatically produced by DockingServer. If you are not satisfied with the images for any reason, you could download the complex structures and visualize them in any molecular viewer. We recommend using Pymol (pymol.sourceforge.net), which can be used for producing publication quality images of the molecular models.
- What are the restrictions in the free version?
- In short: While our software is free, our hardwares are not. Therefore, we cannot grant processor priority and data storage for free users. Our subscribers get higher priority to run molecular modeling jobs, and their own login name to store and organize their data. Moreover, multi-ligand file processing (SDF) is available only for our subscribers because the high processor utilization.
- I used DockingServer in my scientific work. How can I cite it?
- "DockingServer (www.dockingserver.com)", Bikadi Z, Kovacs S, Demko L, Hazai E; Virtua Drug Ltd., Budapest, Hungary (2007)
- What hardware is needed to run dockings by the DockingServer?
- The calculations use our servers, a computer with an ability to run Web browsers and an Internet connection are enough to run calculations.
- What software is needed to run dockings by the DockingServer?
- Molecular modeling and converting softwares run on our servers so you will not need to install any. However, to be able to process the small molecules, you will have to install Java on your computer. It is also recommended that you install a molecular visualisation software, DockingServer is tested to be compatible with Pymol (http://pymol.sourceforge.net).
- What are the hardwares behind the DockingServer?
- Currently DockingServer runs on Dual Quadcore Xeon 2.33GHZ "5345" servers.
- What are the softwares behind the DockingServer?
- Our pipeline software was built on several world-leading applications in the field of molecular modeling. Autodock (http://autodock.scripps.edu), the most popular moleculer docking program is used for molecular docking calculations. Chemaxon tools (www.chemaxon.com) are used for small molecule visualisation and processing. MOPAC2009 (http://openmopac.net) and the revolutionary PM6 semiempirical method can be used to calculate small molecule geometries and electric properties.
- Are the ligands flexible?
- Yes, the ligands are flexible about their single bonds. DockingServer trys to identify the rotatable bonds, which are allowed to rotate freely during the docking runs. If you want to dock rigid ligands, it is possible to change bonds to rigid using the DockingServer.
- Can DockingServer handle multiple-ligand files?
- Yes, Dockingserver is able to automatically convert SDF files to dock-ready form. It is very useful for high-throughput virtual sreening to identify the best compound in small molecule libraries to given targets.
- Are the protein sidechains flexible?
- Currently the whole protein is treated as a rigid molecule. We are intensively working for an easy-to-use method to allow sidechain flexibility, it is expected to be ready within a few months.
- What about protein backbone flexibility?
- Handling protein backbone flexibility during docking calculations is a very difficult task. We are considering the possibilities of how to involve backbone flexibility calculations into the DockingServer.
- Can I dock multiple ligands to the same protein?
- Yes, it is possible. It can be don in subsequent steps: docking the first ligand to the ligand-free protein, then in a second step using the protein with the docked ligand as a target to dock the second ligand.
- How do I measure distances within DockingServer?
- The most important distances for secondary interactions are listed in the docking results section. If you are interested in other distances, you should download the resultant PDB file of the complex structure and measure the distances in a molecule viewer. We recommend using Pymol (pymol.sourceforge.net), which will help you measure distances with ease.
- Is it possible to use Dockingserver for protein-protein docking?
- Currently, protein-protein docking is not possible by DockingServer, however, we are planning to expand the capabilities of Dockingserver to be able to run protein-protein docking jobs.