Journal
PROTEIN SCIENCE
Volume 27, Issue 1, Pages 76-85Publisher
WILEY
DOI: 10.1002/pro.3269
Keywords
membrane proteins; protein complexes; docking; restraint-augmented homology modeling; site-directed spin labeling; distance distributions; ensemble modeling
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Funding
- Swiss National Fund [200020_169057]
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Structural characterization of proteins and their complexes may require integration of restraints from various experimental techniques. MMM (Multiscale Modeling of Macromolecules) is a Matlab-based open-source modeling toolbox for this purpose with a particular emphasis on distance distribution restraints obtained from electron paramagnetic resonance experiments on spin-labelled proteins and nucleic acids and their combination with atomistic structures of domains or whole protomers, small-angle scattering data, secondary structure information, homology information, and elastic network models. MMM does not only integrate various types of restraints, but also various existing modeling tools by providing a common graphical user interface to them. The types of restraints that can support such modeling and the available model types are illustrated by recent application examples.
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