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SCOP2 prototype was a beta version of Structural classification of proteins and classification system that aimed to more the evolutionary complexity inherent in protein structure evolution. [12] It is therefore not a simple hierarchy, but a directed acyclic graph network connecting protein superfamilies representing structural and evolutionary ...
In molecular biology, protein fold classes are broad categories of protein tertiary structure topology. They describe groups of proteins that share similar amino acid and secondary structure proportions. Each class contains multiple, independent protein superfamilies (i.e. are not necessarily evolutionarily related to one another). [1] [2] [3]
A protein superfamily is the largest grouping of proteins for which common ancestry can be inferred (see homology). Usually this common ancestry is inferred from structural alignment [ 1 ] and mechanistic similarity, even if no sequence similarity is evident. [ 2 ]
At the top level are all alpha proteins (domains consisting of alpha helices), all beta proteins (domains consisting of beta sheets), and mixed alpha helix/beta sheet proteins. While most proteins adopt a single stable fold, a few proteins can rapidly interconvert between one or more folds. These are referred to as metamorphic proteins. [5]
Protein domains allow protein classification by a combination of sequence, structure and function, and they can be combined in many ways. In an early study of 170,000 proteins, about two-thirds were assigned at least one domain, with larger proteins containing more domains (e.g. proteins larger than 600 amino acids having an average of more ...
The study of proteins, generally under the heading of proteomics, is a vast and complex subject, and much effort has been made to classify and categorize, according to the many specific fields of investigation under which they come.
Structural Classification of Proteins (SCOP) Protein structure databases CATH database: Protein structure databases ModBase: Sali Lab, UCSF: database of comparative protein structure models Protein model databases SIMAP: database of protein similarities computed using FASTA: Protein model databases Swiss-model: server and repository for protein ...
The CATH Protein Structure Classification database is a free, publicly available online resource that provides information on the evolutionary relationships of protein domains. It was created in the mid-1990s by Professor Christine Orengo and colleagues including Janet Thornton and David Jones , [ 2 ] and continues to be developed by the Orengo ...
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