DDtrek: A PyMOL-Based Management System for 3D Structural Data Series.

Abstract

In multiple areas of molecular biology research, series of closely related atomic structures of biomacromolecules are routinely generated. In particular, rational structure-based drug design heavily relies on the structural analysis of experimentally determined complexes between the target protein and multiple designed ligands (small molecules or biologicals). Here, we introduce DDtrek, a system for alignment, evaluation, and presentation of such structural data. This system is implemented as a plugin for the highly popular molecular graphics software PyMOL. A special feature of DDtrek is visualization of the aligned ligand structures together with the corresponding experimental density maps obtained through X-ray crystallography or cryoelectron microscopy, providing for the assessment of atomic model reliability and partial disorder. DDtrek is a lightweight and user-friendly system that can be utilized by whole research teams. DDtrek is freely available for Windows, MacOS, and Linux from https://github.com/BiocrystLab/DDtrek.