PyRy3D is a software tool for modeling of structures for large macromolecular complexes. It uses Monte Carlo simulation in order to sample conformational space and to identify the best fit complex components structures into a density map of a whole complex with the use of distance restraints derived from experiments.The components (proteins, nucleic acids and any other type of physical objects including e.g. solid surfaces) can be represented as rigid bodies (e.g. based on atomic coordinates of structures determined experimentally or modeled computationally) or as flexible shapes (e.g. for parts, whose structure is dynamic or unknown). The model building procedure applies a Monte Carlo approach to sample the space of solutions. Spatial restraints are used to define components interacting with each other, and a a simple scoring function is applied to pack them tightly into contours of the entire complex (e.g. cryoEM density maps). This approach enables the construction of low-resolution models even for very large macromolecular complexes with components of unknown 3D structure, such as human mitochondrial RNA polymerase gamma.
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