Molecular docking: guidelines to a low-cost methodology

Molecular docking is a powerful tool, given the increasing amount of available protein structures and improved computational tools, but it can become a complicated problem. Caution must be exercised to ensure that the initial point of any docking job suits the purpose of the study at hand. There are several docking methodologies which can be useful in different workflows and this can be confusing to many researchers outside the field, as there are several parameters that must be considered beforehand. In this study, the authors give an overview about our molecular docking protocol and analysis some published results, highlighting key aspects that must be addressed in each step of the process and focusing on what kind of information must be considered before starting a docking job. We focus in freeware software and webservers, resulting in a low-cost methodology that can be easily applied by newcomers to molecular docking.