Creating Coarse-Grained Systems with COBY: Toward Higher Accuracy of Complex Biological Systems.

Current trends in molecular modeling are geared toward increasingly realistic representations of the biological environments reflected in larger, more complex systems. The complexity of the system-building procedure is ideally handled by software that converts user-provided descriptors into system coordinates. This, however, is not a trivial task, as building algorithms use simplifications that result in inaccuracies in the system properties. We created COBY, a coarse-grained system builder that can create a large variety of systems in a single command call with an improved accuracy of the complex membrane and solvent building procedures. COBY also contains features for building diverse systems in a single step, and has functionalities aiding force field development. COBY is an open-source software written in Python 3, and the code, documentation, and tutorials are hosted at https://github.com/MikkelDA/COBY.