Fitting molecular fragments into electron density
- PMID: 18094471
- PMCID: PMC2394793
- DOI: 10.1107/S0907444907033938
Fitting molecular fragments into electron density
Abstract
Molecular replacement is a powerful tool for the location of large models using structure-factor magnitudes alone. When phase information is available, it becomes possible to locate smaller fragments of the structure ranging in size from a few atoms to a single domain. The calculation is demanding, requiring a six-dimensional rotation and translation search. A number of approaches have been developed to this problem and a selection of these are reviewed in this paper. The application of one of these techniques to the problem of automated model building is explored in more detail, with particular reference to the problem of sequencing a protein main-chain trace.
Figures
Similar articles
-
How far are we from automatic crystal structure solution via molecular-replacement techniques?Acta Crystallogr D Struct Biol. 2020 Jan 1;76(Pt 1):9-18. doi: 10.1107/S2059798319015468. Epub 2020 Jan 1. Acta Crystallogr D Struct Biol. 2020. PMID: 31909739 Free PMC article.
-
Rosetta Structure Prediction as a Tool for Solving Difficult Molecular Replacement Problems.Methods Mol Biol. 2017;1607:455-466. doi: 10.1007/978-1-4939-7000-1_19. Methods Mol Biol. 2017. PMID: 28573585 Review.
-
EDM-DEDM and protein crystal structure solution.Acta Crystallogr D Biol Crystallogr. 2009 May;65(Pt 5):477-84. doi: 10.1107/S0907444909008609. Epub 2009 Apr 18. Acta Crystallogr D Biol Crystallogr. 2009. PMID: 19390153 Review.
-
"Conditional Restraints": Restraining the Free Atoms in ARP/wARP.Structure. 2009 Feb 13;17(2):183-9. doi: 10.1016/j.str.2008.12.011. Structure. 2009. PMID: 19217389 Free PMC article.
-
The Buccaneer software for automated model building. 1. Tracing protein chains.Acta Crystallogr D Biol Crystallogr. 2006 Sep;62(Pt 9):1002-11. doi: 10.1107/S0907444906022116. Epub 2006 Aug 19. Acta Crystallogr D Biol Crystallogr. 2006. PMID: 16929101
Cited by
-
Structural and biochemical insights into NEIL2's preference for abasic sites.Nucleic Acids Res. 2023 Dec 11;51(22):12508-12521. doi: 10.1093/nar/gkad1075. Nucleic Acids Res. 2023. PMID: 37971311 Free PMC article.
-
Multivariate estimation of substructure amplitudes for a single-wavelength anomalous diffraction experiment.Acta Crystallogr D Struct Biol. 2023 Apr 1;79(Pt 4):339-344. doi: 10.1107/S2059798323001997. Epub 2023 Mar 28. Acta Crystallogr D Struct Biol. 2023. PMID: 36974967 Free PMC article.
-
Identification and structural analysis of a carbohydrate-binding module specific to alginate, a representative of a new family, CBM96.J Biol Chem. 2023 Feb;299(2):102854. doi: 10.1016/j.jbc.2022.102854. Epub 2022 Dec 31. J Biol Chem. 2023. PMID: 36592931 Free PMC article.
-
ModelCraft: an advanced automated model-building pipeline using Buccaneer.Acta Crystallogr D Struct Biol. 2022 Sep 1;78(Pt 9):1090-1098. doi: 10.1107/S2059798322007732. Epub 2022 Aug 25. Acta Crystallogr D Struct Biol. 2022. PMID: 36048149 Free PMC article.
-
Structural and functional characterization of DdrC, a novel DNA damage-induced nucleoid associated protein involved in DNA compaction.Nucleic Acids Res. 2022 Jul 22;50(13):7680-7696. doi: 10.1093/nar/gkac563. Nucleic Acids Res. 2022. PMID: 35801857 Free PMC article.
References
-
- Bahar, M. et al. (2006). Acta Cryst. D62, 1170–1183. - PubMed
-
- Cohen, S. X., Morris, R. J., Fernandez, F. J., Ben Jelloul, M., Kakaris, M., Parthasarathy, V., Lamzin, V. S., Kleywegt, G. J. & Perrakis, A. (2004). Acta Cryst. D60, 2222–2229. - PubMed
-
- Cowtan, K. (1998). Acta Cryst. D54, 750–756. - PubMed
-
- Cowtan, K. (2001). Acta Cryst. D57, 1435–1444. - PubMed
-
- Cowtan, K. (2006). Acta Cryst. D62, 1002–1011. - PubMed
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources