The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
The Natural History of Protein Domains
Abstract
▪ Abstract Genome sequencing and structural genomics projects are providing new insights into the evolutionary history ofprote in domains. As methods for sequence and structure comparison improve, more distantly related domains are shown to be homologous. Thus there is a need for domain families to be classified within a hierarchy similar to Linnaeus' Systema Naturae, the classification of species. With such a hierarchy in mind, we discuss the evolution of domains, their combination into proteins, and evidence as to the likely origin of protein domains. We also discuss when and how analysis of domains can be used to understand details of protein function. Unconventional features of domain evolution such as intragenomic competition, domain insertion, horizontal gene transfer, and convergent evolution are seen as analogs of organismal evolutionary events. These parallels illustrate how the concept of domains can be applied to provide insights into evolutionary biology.
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Cites
The sequence of the human genome
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Lateral gene transfer and the nature of bacterial innovation
Ochman, H., Lawrence, J. G., & Groisman, E. A. (2000) · Nature · doi:10.1038/35012500 · Cited by 3,816
Gilbert, W. (1986) · Nature · doi:10.1038/319618a0 · Cited by 2,721
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Cited by
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
End-to-End Differentiable Learning of Protein Structure
AlQuraishi, M. (2019) · Cell Systems · doi:10.1016/j.cels.2019.03.006 · Cited by 371
Linear motifs: Evolutionary interaction switches
Neduva, V., & Russell, R. B. (2005) · FEBS Letters · doi:10.1016/j.febslet.2005.04.005 · Cited by 352
Self-citationMore than the sum of their parts: On the evolution of proteins from peptides
Söding, J., & Lupas, A. N. (2003) · BioEssays · doi:10.1002/bies.10321 · Cited by 252
Torruella, G., Derelle, R., Paps, J., Lang, B. F., Roger, A. J., Shalchian-Tabrizi, K., & Ruiz-Trillo, I. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/msr185 · Cited by 169
Nagy, A., Szláma, G., Szarka, E., Trexler, M., Bányai, L., & Patthy, L. (2011) · Genes · doi:10.3390/genes2030449 · Cited by 22
Dissecting the Determinants of Domain Insertion Tolerance and Allostery in Proteins
Mathony, J., Aschenbrenner, S., Becker, P., & Niopek, D. (2023) · Advanced Science · doi:10.1002/advs.202303496 · Cited by 16
A scalable equivariant graph network framework for precise protein function prediction
Ran, Z., Guo, X., Pan, T., Bi, Y., Hao, Y., Sun, H., Song, J., & Li, F. (2025) · Genome Biology · doi:10.1186/s13059-025-03886-y · Cited by 8
Dissecting the Determinants of Domain Insertion Tolerance and Allostery in Proteins
Mathony, J., Aschenbrenner, S., Becker, P., & Niopek, D. (2023) · doi:10.1101/2023.04.11.536407
Metadata
- Authors
- Ponting, C. P., & Russell, R. R.
- Venue
- Annual Review of Biophysics and Biomolecular Structure
- Publisher
- Annual Reviews
- Published
- 2002-06
- Volume
- 31
- Issue
- 1
- Pages
- 45-71
- ISSN
- 1056-8700 (ISSN-L)
- 1545-4266
- OpenAlex
- W2031903428
- Cited by
- 342
- References
- 4
- FWCI
- 6.48
- Type
- journal article
- Language
- en
- Open access
- closed
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