Hello,

(I don't see my 2 last posts, did they be removed or do I just miss them?)

I understood the decision about Autodock was made by research partners.
Would it possible to ask research partners why they don't use Autodock Vina?
Indeed, quoting https://en.wikipedia.org/wiki/AutoDock:
"AutoDock has a successor, AutoDock Vina, which has an improved local search routine and makes use of multicore/multi-CPU computer setups.[3]

AutoDock Vina has been noted for running significantly faster under 64-bit Linux operating systems in several World Community Grid projects that used the software
"
Indeed, there are a lot of crunching projects (included other Covid-19 related), why crunching on non-optimized projects? People CPU/GPUs resource isn't infinite.

Julien

Reminder: The purpose of this thread is to allow as many volunteers as possible to ask questions about the science and technology for OpenPandemics. Thank you to the many volunteers who have asked relevant questions.

If your post has been deleted, it is because of one or more of the following:

Please stay on topic and limit your posts to questions rather than comments so that everyone can easily see the information that will be posted here.

Please review the thread before posting to make sure that your question has not already been asked.

Any volunteer posts that are not questions about the science and technology behind the project will be deleted.

Any volunteer posts that are lengthy comments with a question embedded in the comment, or re-hashes of questions that we have already answered, will also be subject to deletion.

Where/what are the other projects exactly? I only run Rosetta@home here.

Thanks in advance.

Apart from that, to admins: Why is this called a COVID-19 and not a SARS-Cov-2 project?

Thank you as well.

First of all, thanks for the interest in our project! This post is to elaborate on why we opted for AutoDock4 instead of AutoDock Vina.

Both Vina and AutoDock4 are developed in our lab under the AutoDock Suite project. Each has their own advantages, and that is why we keep working with both programs. Generally, docking involves evaluating thousands to millions of conformations and orientations (i.e. poses) of the molecule being docked, before the best result is found. While evaluating a single pose takes approximately the same time in both AutoDock4 and Vina (a few microseconds), Vina is faster because it needs to evaluate fewer poses before reaching the best result. The reasons for this are an efficient search algorithm and a simpler scoring function to describe the interactions.

What Vina gains in performance is lost in flexibility. AutoDock4 allows expert users to tweak the scoring function and define custom potentials. This allows the implementation of very complex protocols and functionalities that would not be possible otherwise. One of these protocols is the Reactive Docking, which is used to model molecules that are able to react with the protein and form a covalent bond. Such molecules are often called suicide inhibitors (a well-known example is penicillin). AutoDock4 can be used to simulate the formation of a chemical bond between a reactive molecule and a protein, thereby predicting if the reaction occurs. A neat feature is that we can implement this protocol without requiring any changes to the code of the program that runs on the WCG, which reduces considerably the effort to use this method without extensive coding efforts on either our end or the IBM side. The Reactive Docking is one of the aspects that make this project unique, because it will allow us to identify suicide inhibitor candidates to be tested by our collaborators.

Besides, for this project we are tuning the search parameters to reduce the number of poses that AutoDock4 evaluates. Our tests show that for some molecules this will bring the runtime of AutoDock4 closer to that of Vina.