Simpkin, Adam J 
ORCID: 0000-0003-1883-9376, Thomas, Jens MH ORCID: 0000-0003-0277-8505, Keegan, Ronan M and Rigden, Daniel J ORCID: 0000-0002-7565-8937
(2022)
<i>MrParse:</i> finding homologues in the PDB and the EBI AlphaFold database tor molecular replacement and more.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 78 (Pt 5).
pp. 553-559.
Abstract
Crystallographers have an array of search-model options for structure solution by molecular replacement (MR). The well established options of homologous experimental structures and regular secondary-structure elements or motifs are increasingly supplemented by computational modelling. Such modelling may be carried out locally or may use pre-calculated predictions retrieved from databases such as the EBI AlphaFold database. MrParse is a new pipeline to help to streamline the decision process in MR by consolidating bioinformatic predictions in one place. When reflection data are provided, MrParse can rank any experimental homologues found using eLLG, which indicates the likelihood that a given search model will work in MR. Inbuilt displays of predicted secondary structure, coiled-coil and transmembrane regions further inform the choice of MR protocol. MrParse can also identify and rank homologues in the EBI AlphaFold database, a function that will also interest other structural biologists and bioinformaticians.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | molecular replacement, AlphaFold2, MrParse, bioinformatic tools, sequence features |
| Divisions: | Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 29 Apr 2022 11:20 |
| Last Modified: | 19 Oct 2023 09:33 |
| DOI: | 10.1107/S2059798322003576 |
| Open Access URL: | https://journals.iucr.org/d/issues/2022/05/00/qn50... |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3154098 |
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