Using Phaser and ensembles to improve the performance of SIMBAD.

ABSTRACT: The conventional approach to search-model identification in molecular replacement (MR) is to screen a database of known structures using the target sequence. However, this strategy is not always effective, for example when the relationship between sequence and structural similarity fails or when the crystal contents are not those expected. An alternative approach is to identify suitable search models directly from the experimental data. SIMBAD is a sequence-independent MR pipeline that uses either a crystal lattice search or MR functions to directly locate suitable search models from databases. The previous version of SIMBAD used the fast AMoRe rotation-function search. Here, a new version of SIMBAD which makes use of Phaser and its likelihood scoring to improve the sensitivity of the pipe

SUBMITTER: Simpkin AJ 

PROVIDER: S-EPMC6939438 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature