Comparison of Free Docking Tools

Abstract

Database of natural medicinal compounds, primarily derived from plants are widely available, distributed and can be accessed for free via the Internet. The protein database that is responsible for a particular disease in molecular biology also has been established since 1971. Limited access of information on results of Indonesian research, repeatability of objects and topics of research are often the case, extract and fraction of medicinal plant resulted nonselective

conclusion of target activity of disease, the lack of advanced research that gained successful outcome due to a very few in number of pure isolates that obtained from certain plants and many other difficulties that will be found in the development of Indonesian medicinal compounds. The insufficiency of research funding given decreased the amount of research and increased competition to get so as to the preliminary studies using prediction theory through computational chemistry is needed to rise the accomplishment of research, one of them is the virtual screening using docking tools. This study aimed to compare the docking tools is available for free. The parameters of comparison are simplicity of use, easiness of access to information, advantages and disadvantages for the novice user, the system that must be prepared, speediness for obtaining and analysing the results and the level of confidentiality. MarvinSketch and OpenBabel are main software that needed for supporting Docking tools. The selected docking tools must be available free for use online or offline. The use of online docking tools that provided by a third-party does not meet the desired level of confidentiality. Dock6, Dock3.7 and PLANTS are not stress-free in the installation or the docking procedure because it needs further experience concerning computer systems. PyRx, Chimera, MarvinSpace or VegaZZ could be selected as a candidate docking tools. They have an easy setup and operation as well as their trustworthy because they can be run offline. Chimera and PyRx recommended as docking tool that have to be used because it has the following advantages: both can be run on any operating system (Windows, Mac or Linux) and fulfil all the requirement. Application of database of natural medicinal compounds and protein targets using docking tool: Chimera and PyRx should be recommended by the Indonesian government in order to become standard procedure of research before performing a certain activity assay of the plant as early prediction approaching the results to be acquired.