General Information
| Description | Automated fold recognition in medium- and low-resolution (4–15 Å) electron density maps |
| Homepage | http://cs.stanford.edu/~mitul/foldEM/ |
Publications
FOLD-EM: automated fold recognition in medium- and low-resolution (4–15 Å) electron density maps
Motivation:
Owing to the size and complexity of large multi-component biological assemblies, the most tractable approach to determining their atomic structure is often to fit high-resolution radiographic or nuclear magnetic resonance structures of isolated components into lower resolution electron density maps of the larger assembly obtained using cryo-electron microscopy (cryo-EM). This hybrid approach to structure determination requires that an atomic resolution structure of each component, or a suitable homolog, is available. If neither is available, then the amount of structural information regarding that component is limited by the resolution of the cryo-EM map. However, even if a suitable homolog cannot be identified using sequence analysis, a search for structural homologs should still be performed because structural homology often persists throughout evolution even when sequence homology is undetectable, As macromolecules can often be described as a collection of independently folded domains, one way of searching for structural homologs would be to systematically fit representative domain structures from a protein domain database into the medium/low resolution cryo-EM map and return the best fits. Taken together, the best fitting non-overlapping structures would constitute a ‘mosaic’ backbone model of the assembly that could aid map interpretation and illuminate biological function.
Result:
Using the computational principles of the Scale-Invariant Feature Transform (SIFT), we have developed FOLD-EM—a computational tool that can identify folded macromolecular domains in medium to low resolution (4–15 Å) electron density maps and return a model of the constituent polypeptides in a fully automated fashion. As a by-product, FOLD-EM can also do flexible multi-domain fitting that may provide insight into conformational changes that occur in macromolecular assemblies.
Availability and implementation:
FOLD-EM is available at: http://cs.stanford.edu/~mitul/foldEM/, as a free open source software to the structural biology scientific community.
Contact:
mitul@cs.stanford.edu or mcmorais@utmb.edu
Supplementary information:
Supplementary data are available at Bioinformatics online.
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