MrParse: finding homologues in the PDB and the EBI AlphaFold database for molecular replacement and more. Issue 5 (26th April 2022)

• Record Type: Journal Article
• Authors: Simpkin, Adam J.; Thomas, Jens M. H.; Keegan, Ronan M.; Rigden, Daniel J.
• Is Part Of: Acta crystallographica. Volume 78:Issue 5(2022)
• Page Start: 553
• Page End: 559
• Publication Date: 2022-04-26
• Subjects: molecular replacement -- AlphaFold2 -- MrParse -- bioinformatic tools -- sequence features; X-ray crystallography -- Periodicals; Crystallography -- Periodicals; Molecular biology -- Periodicals; Molecular structure -- Periodicals; Biomolecules -- Structure -- Periodicals; Cytology -- Periodicals; Biomolecules -- Structure; Crystallography; Cytology; Molecular biology; Molecular structure; X-ray crystallography; Periodicals; 548
• DOI: 10.1107/S2059798322003576
• Languages: English
• ISSNs: 2059-7983

Abstract

Abstract : MrParse is a software package designed to aid decision making in molecular replacement (MR). It performs a sequence search to find search models, not only in the PDB, as would conventionally be performed, but also in the EBI AlphaFold database, and provides a series of analyses relevant to MR such as crystal pathology detection and sequence analysis. 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.