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. 2020 Jan 1;76(Pt 1):1-8.
doi: 10.1107/S2059798319015031. Epub 2020 Jan 1.

Using Phaser and ensembles to improve the performance of SIMBAD

Adam J Simpkin  1 , Felix Simkovic  1 , Jens M H Thomas  1 , Martin Savko  2 , Andrey Lebedev  3 , Ville Uski  3 , Charles C Ballard  3 , Marcin Wojdyr  4 , William Shepard  2 , Daniel J Rigden  1 , Ronan M Keegan  1
Affiliations

Using Phaser and ensembles to improve the performance of SIMBAD

Adam J Simpkin et al. Acta Crystallogr D Struct Biol. .

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 pipeline is presented. It is shown that the additional compute time potentially required by the more sophisticated scoring is counterbalanced by the greater sensitivity, allowing more cases to trigger early-termination criteria, rather than running to completion. Using Phaser solved 17 out of 25 test cases in comparison to the ten solved with AMoRe, and it is shown that use of ensemble search models produces additional performance benefits.

Keywords: SIMBAD; contaminants; ensembles; molecular-replacement pipeline; sequence independent; structure solution.

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Figures

Figure 1
Figure 1
Flowchart detailing the new Phaser pathways (shown with pink arrows) that have been implemented in SIMBAD. Criteria for a solution are R values of <0.45 from REFMAC5 and/or an LLG of >60 and TFZ of >8 if MR is performed using Phaser. SIMBAD will use the MR subroutine to test the top 200 solutions ranked by AMoRe Z-score or Phaser RFZ score unless a solution has been identified by the early-termination procedure. The early-termination procedure is triggered when a search model achieves a Z-score of >10 in an AMoRe search or an RFZ of >7 in a Phaser search. This search model is tested using the MR subroutine and if the placed model meets the criteria for a solution then the process will terminate early.
Figure 2
Figure 2
Venn diagram comparing the number of solutions and the average r.m.s.d. of successful search models obtained from the 19 test cases (known to be solvable) using the default AMoRe rotation search and the Phaser rotation search in several differing configurations. As mentioned in the text, two of the 19 cases were not solved in any run even when using the best available search model. Not shown here are the six cases that we were unable to solve using the closest available search model.
Figure 3
Figure 3
3D bar chart showing the ranking of successful search models using AMoRe and Phaser with various parameters. The bars are coloured using a rainbow scale where violet indicates a successful search model that has ranked top in the search and red indicates that the highest ranking potentially successful search model lay outside the top 200. As only the top 200 search models are trialled in the MR step, those models which ranked higher than 200 represent unsuccessful searches.
Figure 4
Figure 4
(a) The MoRDa domain (PDB entry 2i82; magenta) aligned with the crystal structure (PDB entry 5uba; rainbow). (b) The MrBUMP-derived truncated ensemble (PDB entry 2i82; magenta) aligned with the crystal structure (PDB entry 5uba; rainbow).
See this image and copyright information in PMC

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