Assembline

Assembline is an assembly line of macromolecular assemblies!

Assembline is a multi-step protocol for integrative structural modeling of macromolecular complexes based on electron microscopy, cross-linking mass spectrometry and other data. The protocols is based on our Xlink Analyzer and external software: Integrative Modeling Plafform (IMP), Python Modeling Interface (PMI), UCSF Chimera, and imp-sampcon. Comparing to other methods, Assembline enables efficient sampling of conformational space through a multi-step procedure, provides new modeling restraints, and includes a unique configuration system for setting up the modelling project.

Code

• Assembline installation package for Anaconda
• Assembline code
• Installation instructions and manual

Tutorials

• Elongator complex (good for start)
• Yeast nuclear pore complex (rather a big thing)

How to cite

If you use this software, please cite it along the dependencies it uses internally, at least:

• Rantos V., Karius K., and Kosinski J. Integrative structural modeling of macromolecular complexes using Assembline, Nature Protocols, 2021
• Integrative Modeling Plafform (IMP)
• Python Modeling Interface (PMI)
• UCSF Chimera
• Kosinski, J., et al. Xlink Analyzer: Software for analysis and visualization of cross-linking data in the context of three-dimensional structures. J. Struct. Biol. (2015)
• imp-sampcon tool used for analysis

Contact:

Please do not hesitate to send requests, comments and bug reports to:
Jan Kosinski, [email protected]