Molecular Docking: Considerations of a Low Cost and Suitable Methodology and Some Successful Applications

Molecular docking can be a powerful tool, given the growing amount of available solved protein crystallographic structures and always improving computational tools but it can also develop in a more complex issue than one would initially imagine. The reasoning behind this statement comes from the simple fact that even if a good amount of data is readily available, care should be taken to ensure that the starting point of any docking job suits the purpose of the study at hand. There are several docking methodologies which can be useful in one or another work flow and to many researchers outside the field this can be elusive as there are several parameters that must be addressed beforehand. In the present study, the authors give an overview about our molecular docking protocol and analysis of the results, highlighting key aspects that must be addressed in each step of the process and setting the reader's mind to focus on what kind of information have to be considered before starting a docking job. Our focus is towards freeware software and web servers, resulting in a virtually free methodology that can be easily applied by newcomers to molecular docking. Also, examples of successful docking applications are given.