PyRy3D is a user-friendly computational method for building structural models of mutltisubunit macromolecular complexes by a hybrid approach.

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A software tool for modeling of large macromolecular complexes

PyRy3D server is available!

We encourage you to run modeling tasks with our web server. Go to PYRY SERVER subsite or follow the link.


Meet us at PyRy3D workshops!

1. We are pleased to invite you to participate in the workshop "Structural Modeling for Large Macromolecular Complexes" (second edition), which will be held on 27-30.04.2015 in Oeiras, Portugal.The course will be conducted by PyRy3D developers: Joanna Kasprzak and Mateusz Dobrychłop. Program and detailed description are available here:


2. We are pleased to invite you to participate in the workshop "Structural Modeling for Large Macromolecular Complexes", which will be held on 11-13.06.2014 in Oeiras, Portugal.The course will be conducted by researchers from the International Institute of Molecular and Cell Biology in Warsaw, Joanna Kasprzak (PyRy3D author) and Grzegorz Chojnowski. Deadline for registration is 15.05.2014 and detailed information can be found at:


We would also greatly appreciate if you could forward this announcement to anybody who may be interested.

3. PyRy3D program will also be presented during ECCB'14 conference in Strasbourg. Grzegorz Chojnowski will give a tutorial  "W16 - Workshop on Tools and Techniques for Analysis and Design of Macromolecular Structures". For more details plese visit the workshop website:



What is PyRy3D?

One of the major challenges in structural biology is to determine the structures of macromolecular complexes and to understand their function and mechanism of action. However, structural characterization of macromolecular assemblies is very difficult. A hybrid computational approach is required that will be able to incorporate spatial information from a variety of experimental methods into modeling procedure. Thus far, we developed PyRy3D, a method for building low-resolution models of large macromolecular complexes. 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.




Why is PyRy3D interesting?


PyRy3D program was classified as one of the top three finalists during The ISMB 2011 Killer Application Award Competition, where a committee selects tools or systems of most practical benefit to biochemists and/or molecular biologists. To be eligible for the Killer Application Award, a system or a tool must also be fully functional, and be presented at the ISMB 2011 conference. Several scientists in their modelling tasks have already successfully used PyRy3D, and some opinions about the program can be found at users opinions subpage

PyRy3D can be integrated with user's code via Python scripts. The program is also supported by UCSF Chimera Extension which provides users with graphical interface for the program.

If you are interested in PyRy3D please visit Tutorial Tutorial and/or the Frequently Asked Questions.





2015/04/27-30 - PyRy3D workshop in Oeiras, Portugal; register NOW!
2014/07/18 - PyRy3D workshop during ECCB conference