Flexible fitting of AlphaFold2-predicted models to cryo-EM density maps using elastic network models: a methodical affirmation

ModeHunter: A Package for the Reductionist Analysis, Animation, and Application of Elastic Biomolecular Motion

ModeHunter is a modular Python software package for the simulation of 3D biophysical motion across spatial resolution scales using modal analysis of elastic networks. It has been curated from our in-house Python scripts over the last 15 years, with a focus on detecting similarities of elastic motion between atomic structures, coarse-grained graphs, and volumetric data obtained from biophysical or biomedical imaging origins, such as electron microscopy or tomography. With ModeHunter, normal modes of biophysical motion can be analyzed with various static visualization techniques or brought to life by dynamics animation in terms of single or multimode trajectories or decoy ensembles. Atomic structures can also be refined against volumetric densities with flexible fitting strategies. The software consists of multiple stand-alone programs for the preparation, analysis, visualization, animation, and refinement of normal modes and 3D data sets. At its core, two spatially reductionist elastic motion engines are currently supported: elastic network models (typically for a Cα level of detail and rectangular meshes) and bend-twist stretch (for trigonal or tetrahedral meshes or trees resulting from spatial clustering). The programs have recently been modernized to Python 3, requiring only the common numpy and scipy external libraries for numerical support. The main advantage of our modular design is that the tools can be combined by the end users for specific modeling applications, either standalone or with complementary tools from our C/C++-based Situs modeling package. The modular design and consistent look and feel facilitate the maintenance of individual programs and the development of novel application workflows. Here, we provide the first complete overview of the ModeHunter package as it exists today, with an emphasis on functionality and workflows supported by version 1.4.