RxTx Research is utilizing the latest computational biochemical and biophysical scientific findings to develop the next generation open-source software for academic and industrial applications.
We held talks about RxDock at University of Auckland School of Chemical Sciences and University of Rijeka Department of Biotechnology seminars. The recordings are embedded below.
At RxTx, we develop our solutions by using and extending free and open-source software. We strongly believe in keeping the software free and open source as we use, modify, and enhance it to fit our needs. RxDock is a fork of rDock, a fast, versatile and open-source (LGPLv3) program for docking ligands to proteins and nucleic acids. For a non-developer perspective, see the documentation linked below. For a developers perspective, read on.
The original rDock started in the late 1990s and RxDock forked from it in 2019. Considering the speed of software evolution, that time points are several lifetimes apart in the world of software development. Some wrinkles here and there in code are to be expected and, while we at RxTx and the community around us are very busy ironing these wrinkles, they admittedly are there. The primary target systems for RxDock are Linux on AMD64 (x86-64) with the GCC compiler as well as FreeBSD on AMD64 with the Clang compiler.
RxDock should become the high-throughput virtual screening engine for workstations, high performance computers, and the cloud. The goal of this project was to evolve the molecular docking code for running on modern computers, including supercomputers and clouds.
The source code has been modernized using C++11 and beyond. Continuing the great work done by the rDock project, RxDock is using Meson for building and automatically downloading missing or outdated dependencies as wrapped libraries. Testing is now done with Google Test, linear algebra is powered by Eigen, and random number generation by PCG. OpenMP has been used to speed up cavity search. Documentation is written in reStructuredText and built by Sphinx, while API documentation is built by Doxygen. There are many other smaller changes; if you are interested in details, until the release notes are written we invite you to check the project commit history on GitLab or GitHub for details.
The development of a streamlined command-line interface using cxxopts was started during the project. Development of graphical and web user interfaces are planned in future projects.