The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
The Bio3D packages for structural bioinformatics
Open accessAbstract
Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and dynamics. Major functionality includes biomolecular database searching and retrieval, sequence and structure conservation analysis, ensemble normal mode analysis, protein structure and correlation network analysis, principal component, and related multivariate analysis methods. Here, we review recent package developments, including a new underlying segregation into separate packages for distinct analysis, and introduce a new method for structure analysis named ensemble difference distance matrix analysis (eDDM). The eDDM approach calculates and compares atomic distance matrices across large sets of homologous atomic structures to help identify the residue wise determinants underlying specific functional processes. An eDDM workflow is detailed along with an example application to a large protein family. As a new member of the Bio3D family, the Bio3D‐eddm package supports both experimental and theoretical simulation‐generated structures, is integrated with other methods for dissecting sequence‐structure–function relationships, and can be used in a highly automated and reproducible manner. Bio3D is distributed as an integrated set of platform independent open source R packages available from: http://thegrantlab.org/bio3d/.
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Cites
Crystal structure of the β2 adrenergic receptor–Gs protein complex
Rasmussen, S. G. F., DeVree, B. T., Zou, Y., Kruse, A. C., Chung, K. Y., Kobilka, T. S., Thian, F. S., Chae, P. S., Pardon, E., Calinski, D., et al. (2011) · Nature · doi:10.1038/nature10361 · Cited by 3,009
Cited by
AlphaFold2 models indicate that protein sequence determines both structure and dynamics
Guo, H.-B., Perminov, A., Bekele, S., Kedziora, G., Farajollahi, S., Varaljay, V., Hinkle, K., Molinero, V., Meister, K., Hung, C., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-14382-9 · Cited by 248
The Birth-and-Death Evolution of Cytochrome P450 Genes in Bees
Darragh, K., Nelson, D. R., & Ramírez, S. R. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab261 · Cited by 27
Guo, H.-B., Varaljay, V. A., Kedziora, G., Taylor, K., Farajollahi, S., Lombardo, N., Harper, E., Hung, C., Gross, M., Perminov, A., et al. (2023) · Scientific Reports · doi:10.1038/s41598-023-30310-x · Cited by 22
AlphaFold2 modeling and molecular dynamics simulations of an intrinsically disordered protein
Guo, H.-B., Huntington, B., Perminov, A., Smith, K., Hastings, N., Dennis, P., Kelley-Loughnane, N., & Berry, R. (2024) · PLOS ONE · doi:10.1371/journal.pone.0301866 · Cited by 13
Metadata
- Authors
- Grant, B. J., Skjærven, L., & Yao, X.
- Venue
- Protein Science
- Publisher
- Wiley
- Published
- 2020-08-17
- Volume
- 30
- Issue
- 1
- Pages
- 20-30
- ISSN
- 0961-8368 (ISSN-L)
- 1469-896X
- OpenAlex
- W3046468150
- Cited by
- 462
- References
- 1
- FWCI
- 10.86
- Type
- journal article
- Language
- en
- Open access
- bronze
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