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Appying a novel web-tool for performing virtual screening experiments
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1  Universidade Federal do Rio Grande - FURG


The use of in-silico methods for identifying new drugs to a target of interest is a step of a process called Rational Drug Design. This process consider a target protein, also known as receptor, which the three-dimensional structure is use to determine the binding site, and a set of drug candidates that are tested in order to establish a stable complex. The in-silico analysis of a set of drug candidates is performed by a computational technique defined as Virtual Screening (VS). In a previous work we developed a novel web tool for  configuring different types of VS experiments using AutoDock Vina docking software. The presented tool is a framework that generates a python script to run a VS experiment in the users’ computer according to the users configuration on the framework web interface. In this paper we propose to apply the developed framework to a specific VS experiment considering one target receptor and a set of ligands. For this VS experiment the researcher informs the location of receptor and ligands files as well as their formats. It is also possible to set receptor and ligand flexibility.  After this, the user indicates the output folder where all the results in the user’s computer will be stored after the script execution.  Then, the user should configure the box area that indicates where ligands will be docked in the receptor molecule. The box size and the center must be configured, the variation of box center could be configured if user wants to execute an experiment that search the binding site in all molecule. For results analysis, the framework uses LigPlot software that describes the interactions between ligand and receptor amino-acids atoms after the performed molecular docking. In this way, this paper demonstrates the usage of the proposed framework for VS where we considered as receptor the structure of the human voltage-dependent anion channel (PDB code: 2JK4) and as ligands different types of carbon nanotubes. In the performed experiment we defined both receptor and ligands as rigid and considered only one box for representing the receptor binding site.

Keywords: Protein Data Bank, Virtual Screening, Rational Drug Design, Molecular Docking
Comments on this paper
Ihosvany Camps
Did you implemented a protein preparation protocol? Something to add hydrogens, correct they position, fix missing residues, etc.?

Vinicius Seus
To prepare the protein, it is necessary to be installed the MGLTools and inform it in the form. This way, the molecule will be converted to pdbqt format and then this molecule will receive charges. But I dont have something implemented to deal with this missing residues and positions.