Journal
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
Volume 4, Issue 1, Pages 28-39Publisher
IEEE COMPUTER SOC
DOI: 10.1109/TCBB.2007.1003
Keywords
structural bioinformatics; intermediate resolution cryo-EM maps; 3D alignment of secondary structures; macromolecular assemblies; cyclic symmetry
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Funding
- Intramural NIH HHS Funding Source: Medline
- NCI NIH HHS [N01-CO-12400] Funding Source: Medline
- NATIONAL CANCER INSTITUTE [Z01BC010442, Z01BC010441] Funding Source: NIH RePORTER
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Cryo-EM has become an increasingly powerful technique for elucidating the structure, dynamics, and function of large flexible macromolecule assemblies that cannot be determined at atomic resolution. However, due to the relatively low resolution of cryo-EIM data, a major challenge is to identify components of complexes appearing in cryo-EM maps. Here, we describe EMatch, a novel integrated approach for recognizing structural homologues; of protein domains present in a 6-10 angstrom resolution cryo-EM map and constructing a quasi-atomic structural model of their assembly. The method is highly efficient and has been successfully validated on various simulated data. The strength of the method is demonstrated by a domain assembly of an experimental cryo-EM map of native GroEL at 6 angstrom resolution.
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