MrParse : finding homologues in the PDB and the EBI AlphaFold database for molecular replacement and more
Open accessPublished version of a preprint
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.
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Cites
Highly accurate protein structure prediction with AlphaFold
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AlphaFold, Artificial Intelligence (AI), and Allostery
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Understanding a protein fold: The physics, chemistry, and biology of α-helical coiled coils
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- Authors
- Simpkin, A. J., Thomas, J. M. H., Keegan, R. M., & Rigden, D. J.
- Affiliations
- University of Liverpool (GB)
- Rutherford Appleton Laboratory (GB)
- Corresponding author
- Rigden, Daniel J.
- Venue
- Acta Crystallographica Section D Structural Biology
- Published
- 2022-04-26
- Volume
- 78
- Issue
- 5
- Pages
- 553-559
- ISSN
- 2059-7983 (ISSN-L)
- PMC
- PMC9063843
- OpenAlex
- W4225390182
- Cited by
- 24
- References
- 6
- Citations by year
- 2025: 2 · 2024: 11 · 2023: 7 · 2022: 4
- FWCI
- 1.69
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Acta Crystallographica Section D Structural Biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- ePubs (Science and Technology Facilities Council, Research Councils UK) (submittedVersion)
- Funders
- Biotechnology and Biological Sciences Research Council (BB/S007105/1)
- Topics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Inorganic Chemistry › Crystal structures of chemical compounds
- Keywords
- molecular replacement, AlphaFold, secondary structure prediction, transmembrane region prediction, crystal structure solution, protein structure prediction
- MeSH terms
- Protein Domains, Models, Molecular, Proteins, Protein Structure, Secondary, Databases, Protein
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