Helical ensembles outperform ideal helices in molecular replacement.

ABSTRACT: The conventional approach in molecular replacement is the use of a related structure as a search model. However, this is not always possible as the availability of such structures can be scarce for poorly characterized families of proteins. In these cases, alternative approaches can be explored, such as the use of small ideal fragments that share high, albeit local, structural similarity with the unknown protein. Earlier versions of AMPLE enabled the trialling of a library of ideal helices, which worked well for largely helical proteins at suitable resolutions. Here, the performance of libraries of helical ensembles created by clustering helical segments is explored. The impacts of different B-factor treatments and different degrees of structural heterogeneity are explored. A 30% increase

SUBMITTER: Sanchez Rodriguez F 

PROVIDER: S-EPMC7543657 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature