Molecular Docking with Open Access Software
The last couple of years have disrupted classes for many students, I helped devise a course for MRes students at UCL undertake a computational drug discovery project using open source tools. A pleasure to work with a group of really bright and enthusiastic group of students
The workflow has now been written up as a Lab Manual which is available for anyone to use.
The publication describing the work is now available (Open Access) Molecular Docking with Open Access Software: Development of an Online Laboratory Handbook and Remote Workflow for Chemistry and Pharmacy Master’s Students to Undertake Computer-Aided Drug Design DOI.
In response to the closure of many university laboratories due to the Covid-19 pandemic in 2020, a handbook and remote webinar approach designed to support students in the use of software tools for computer-aided drug design has been developed. Specifically, the course has been designed for chemistry and pharmacy students who have little or no experience of computational techniques and can use open-source software on their own machines. In this way a flexible and relevant course, giving a rigorous academic experience, could be delivered even in the most challenging of circumstances. We believe that this laboratory protocol will help to “democratize” the scientific process in this field.
The lab Manual is available in a GitHub repository. https://github.com/UCL/OpenDockingLab_Handbook.
This repository is the place to store and edit the lab handbook for UCL teaching courses that involve the use of open source tools in molecular docking.
Files currently available are shown above, on this "code" tab. The most recent version of the lab manual is there, for download and the manual is also available in full on the wiki as a living document that can be updated by anyone, year on year. If you'd like to suggest edits it's easy to do that by opening an Issue (tab above).
We'd love to hear of new docking tools or scoring functions that we could include.
Feel free to contribute.
You might also be interested in the RSC CICAG YouTube channel https://www.youtube.com/c/RSCCICAG that contains many workshops highlighting Open Source tools for Chemistry.