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User interface through which widgets can be created.
Allows users to work with multiple data sets and build pipelines.
Easy to use.
All files work on Windows and Linux.
Windows and Linux versions are available for download.
Once you've opened the program the first thing you need to do is create a main data file and rename it to "main.dat". The first column contains information about the widget's data files, like the type of data, width and height of the widget.
The second column contains the paths of the data files that we want to work with. This data is automatically read into a separate widget, called the "data" widget.
The third column contains the names of each data set. By default, all data sets are called "file_name" where "file_name" is the name of each file. Users can rename files to whatever they want.
The next step is to create widgets. A widget is the visual representation of a data set, for example, everything that appears in a tabbed window.
Buttons appear in the tabbed window, where users can create a separate widget. Widgets can appear as a popup window, tabbed window or floating window.
Users can create links between widgets by dragging from one widget to another. The selection looks like a straight line. For example, the start of the line starts on the left and the end of the line on the right.
To avoid confusion, users can name a link "weld" or "reaction". A line is actually the "reaction" and the area in between is the "weld". When users double-click on the link, an arrow appears in the middle of it and it glows red or yellow.
Through the double-click of links, users can create new widgets. As an example, the "weld" of the "reaction" will be available in a popup window with the rest of the data set.
Users can add any additional parameter to a widget by clicking on it and selecting the parameters tab.
When users save the links and data, the application will open up a window with all of the information they've worked with. Users can edit the window's properties directly or choose to save it as a scheme. Schemes and links are the same as widgets, with the only difference being that they don't have the parameter tab.
Schemes can appear in the main window as a popup window, tabbed window or a floating window
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Autodock is a free e-learning package that delivers tutorials and a workbench for molecular docking simulations. It also offers the possibility of incorporating 3D molecular structures to the analysis of the interactions.
At the moment the site focuses on simpler tasks such as the preparation of the input data files, the selection of the binding site and possible receptors and ligands, but it also includes a workflow for the docking simulations that should be easier to follow, once you understand the basic setup.
Getting it
For people who want to download a version for their computer, they can go directly to the download page, but if you just want to install it, you can navigate to the ZIP file and get it that way.
A big thank to everyone who contributed by sending the tutorials by email, so I could include them in this review.
Features
In this section I'll describe what Autodock can do for you, along with the objectives that you can achieve using it.
The main objective of Autodock
The main objective of the package is to make people understand what is a molecular docking simulation and how to prepare molecules for it.
It provides a fast and easy access to the sites that you can use for free, it also allows you to estimate if your structure is an antagonist, a potential agonist or a neutral molecule.
Now that you know what the package can do, it's time to start!
How to get started
Autodock starts by asking you to do the pre-requisite checks in a simple way.
For example, if you want to use a 3D structure file, you have to enter the coordinates of the atoms, so Autodock checks if the file is VDW (van der Waals) compliant, without having to convert it in a format that is compatible with the system.
You are also asked to save the structure in a format that will be used by the software, along with the name of the file that you want to use for the pre-step data input.
All the checks are simple and you can do them as they are shown.
Select the pre-steps
Once you have completed all of the checks, you have to select what is going to be done to your structure.
At this point, you have to work with the molecules that you are going to use as receptor and / or ligand. In fact, before you start working with your molecules, Autodock prepares them in the active step,
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