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Exploiting structural classifications for function prediction: towards a domain grammar for protein function.
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2
Protein families and their evolution-a structural perspective.
Annu Rev Biochem. 2005;74:867-900. doi: 10.1146/annurev.biochem.74.082803.133029.
3
Classification of proteins: available structural space for molecular modeling.
Methods Mol Biol. 2012;857:1-31. doi: 10.1007/978-1-61779-588-6_1.
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Review: what can structural classifications reveal about protein evolution?
J Struct Biol. 2001 May-Jun;134(2-3):145-65. doi: 10.1006/jsbi.2001.4398.
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A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary.
Protein Sci. 2003 Oct;12(10):2150-60. doi: 10.1110/ps.0306803.
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Population statistics of protein structures: lessons from structural classifications.
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Classification of protein functional surfaces using structural characteristics.
Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1170-5. doi: 10.1073/pnas.1119684109. Epub 2012 Jan 11.
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The Classification of Protein Domains.
Methods Mol Biol. 2017;1525:137-164. doi: 10.1007/978-1-4939-6622-6_7.
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CATH--a hierarchic classification of protein domain structures.
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Clustering protein functional families at large scale with hierarchical approaches.
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Comparative Evolutionary Genomics in Insects.
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A unified statistical model of protein multiple sequence alignment integrating direct coupling and insertions.
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Common Amino Acid Subsequences in a Universal Proteome--Relevance for Food Science.
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Functional classification of CATH superfamilies: a domain-based approach for protein function annotation.
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INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity.
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CATH FunFHMMer web server: protein functional annotations using functional family assignments.
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Biophysical constraints on the evolution of tissue structure and function.
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Effective moment feature vectors for protein domain structures.
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本文引用的文献

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Turning a hobby into a job: how duplicated genes find new functions.
Nat Rev Genet. 2008 Dec;9(12):938-50. doi: 10.1038/nrg2482.
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Just how versatile are domains?
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Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.
PLoS Comput Biol. 2008 Aug 1;4(8):e1000142. doi: 10.1371/journal.pcbi.1000142.
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Arrangements in the modular evolution of proteins.
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Biochemistry. Metamorphic proteins.
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Exploring the structure and function paradigm.
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Cradle-loop barrels and the concept of metafolds in protein classification by natural descent.
Curr Opin Struct Biol. 2008 Jun;18(3):358-65. doi: 10.1016/j.sbi.2008.02.006. Epub 2008 May 3.
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Characterization and prediction of residues determining protein functional specificity.
Bioinformatics. 2008 Jul 1;24(13):1473-80. doi: 10.1093/bioinformatics/btn214. Epub 2008 May 1.
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Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments.
Proc Natl Acad Sci U S A. 2008 Apr 8;105(14):5441-6. doi: 10.1073/pnas.0704422105. Epub 2008 Apr 2.

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