Overview of Questions 

 

 

Answers

Is VirtualFlow free to use?

Yes, VirtualFlow can be used by anyone without costs. 

 

Can I use VirtualFlow as a non-computational scientist?

Yes, but you may need to put some effort into it to learn the required skills, in particular,:

  • Linux/Bash: You should be comfortable with using the Linux command line, in particular Bash. There are many online tutorials available, such as this one.
  • Linux Clusters/Resource managers: You need to be comfortable with using the cluster you want to use, in particular its resource manager (such as SLURM). Often, the institution which provides/manages the cluster regularly offers free user training sessions for beginners which one can take part in.
  • VirtualFlow: You need to understand how VirtualFlow works, and how to use it. Many aspects are described in the official documentation. 

If you have no experience so far with Linux, the command line, and computer clusters, then it might take one or two weeks to learn these required basic skills and VirtualFlow to arrive at a stage where you will be able to use VirtualFlow in a productive manner.

If you have experience with Linux and Clusters, then it might only take two or three days to understand VirtualFlow sufficiently well and to use it with high efficiency.

 

Is VirtualFlow open source?

Yes, VirtualFlow is open source, published under the GNU GPL.

 


Can I contribute to/join the VirtualFlow project?

Yes, we warmly welcome interested researchers to join the project and/or contribute in one of many ways, such as:

  • Improvements of the quality of the current code
  • Improvements or extensions of the documentation
  • Resolution of one of the issues on Github
  • Extension of the code with by adding new features
  • Creation of new versions of VirtualFlow for other types of tasks

 

Is VirtualFlow difficult to install?

Regarding the VirtualFlow package files themselves, the installation is relatively simple. The package files can be installed within minutes by simply unpacking a tar-archive or by cloning the GitHub repo.

In particular, VFVS should be directly ready to use (unless ADFR is used as the docking program, which needs to be installed by the user separately).

VFLP requires additional packages to be installed. And since each cluster and cloud computing platform is different, at times there can be smaller complications with certain aspects, such as the job files which may need to be adjusted. However, computing infrastructures/clusters usually have admins available who can help with unexpected issues, in case some should arise. 

 

What requirements does VirtualFlow have?

VirtualFlow runs on any computing infrastructure which is managed by a batch system (resource manager). These are Linux mainly computer clusters, as well as cloud computing platforms (since resource manages can run on top of them).

Most academic institutions provide Linux clusters to their members free of charge.

Almost any supercomputer is also just a large Linux cluster. National supercomputing centers often allow applying for computing time without costs.

 

How are the REAL Library of Enamine and the ZINC15 database related?

The ZINC15 database contains compounds from many different vendors and other catalogs of compounds which are not commercially available (and thus can't be ordered). Most of the compounds in the ZINC15 database are not yet in a ready-to-dock format. At the time of writing, only around 450 million molecules are provided in a ready-to-dock format. Some of them are from the REAL Library from Enamine, but other compounds of this set are from other vendors. Thus, the ZINC15 database provides only a fraction of the REAL Library from Enamine in a ready-to-dock format. 

The REAL Library which we provide comes from a single vendor, Enamine. This has many advantages, such as having to deal only with a single vendor, and being sure that the compounds are contained in a commercial vendor catalog. Also, we provide the full REAL Library with over 1.4 billion compounds (and it is a later version than the one contained in the ZINC15 database).

 

How can I cite VirtualFlow or the VirtualFlow ligand libraries?

Please cite the following publications:

  • Gorgulla, C., Boeszoermenyi, A., Wang, Z. et al. An open-source drug discovery platform enables ultra-large virtual screens. Nature (2020). https://doi.org/10.1038/s41586-020-2117-z

  • Gorgulla, C., Fackeldey, K., Wagner, G., & Arthanari, H. (2020). Accounting of Receptor Flexibility in Ultra-Large Virtual Screens with VirtualFlow Using a Grey Wolf Optimization Method. Supercomputing Frontiers and Innovations, 7(3), 4–12. https://doi.org/10.14529/jsfi200301