MrParse: finding homologues in the PDB and the EBI AlphaFold database for molecular replacement and more.
AlphaFold2
MrParse
bioinformatic tools
molecular replacement
sequence features
Journal
Acta crystallographica. Section D, Structural biology
ISSN: 2059-7983
Titre abrégé: Acta Crystallogr D Struct Biol
Pays: United States
ID NLM: 101676043
Informations de publication
Date de publication:
01 May 2022
01 May 2022
Historique:
received:
31
08
2021
accepted:
29
03
2022
entrez:
3
5
2022
pubmed:
4
5
2022
medline:
6
5
2022
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 35503204
pii: S2059798322003576
doi: 10.1107/S2059798322003576
pmc: PMC9063843
doi:
Substances chimiques
Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
553-559Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/S007105/1
Pays : United Kingdom
Informations de copyright
open access.
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