FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2149361608> ?p ?o ?g. }

• W2149361608 abstract "For most proteins in the genome databases, function is predicted via sequence comparison. In spite of the popularity of this approach, the extent to which it can be reliably applied is unknown. We address this issue by systematically investigating the relationship between protein function and structure. We focus initially on enzymes classified by the Enzyme Commission (EC) and relate these to structurally classified proteins in the SCOP database. We find that the major SCOP fold classes have different propensities to carry out certain broad categories of functions. For instance, alpha/beta folds are disproportionately associated with enzymes, especially transferases and hydrolases, and all-alpha and small folds with non-enzymes, while alphaa beta folds have an equal tendency either way. These observations for the database overall are largely true for specific genomes. We focus, in particular, on yeast, analyzing it with many classifications in addition to SCOP and EC (i.e. COGs, CATH, MIPS), and find clear tendencies for fold-function association, across a broad spectrum of functions. Analysis with the COGs scheme also suggests that the functions of the most ancient proteins are more evenly distributed among different structural classes than those of more modern ones. For the database overall, we identify the most versatile functions, i.e. those that are associated with the most folds, and the most versatile folds, associated with the most functions. The two most versatile enzymatic functions (hydro-lvases and O-glycosyl glucosidases) are associated with seven folds each. The five most versatile folds (TIM-barrel, Rossmann, ferredoxin, alpha-beta hydrolase, and P-loop NTP hydrolase) are all mixed alpha-beta structures. They stand out as generic scaffolds, accommodating from six to as many as 16 functions (for the exceptional TIM-barrel). At the conclusion of our analysis we are able to construct a graph giving the chance that a functional annotation can be reliably transferred at different degrees of sequence and structural similarity. Supplemental information is available from http://bioinfo.mbb.yale.edu/genome/foldfunc. # 1999 Academic Press" @default.
• W2149361608 created "2016-06-24" @default.
• W2149361608 creator A5042321575 @default.
• W2149361608 creator A5077758303 @default.
• W2149361608 date "1999-01-01" @default.
• W2149361608 modified "2023-09-27" @default.
• W2149361608 title "The Relationship Between Protein Structure and Function: A Comprehensive Survey Focusing on Enzymes" @default.
• W2149361608 cites W1483008427 @default.
• W2149361608 cites W1508885706 @default.
• W2149361608 cites W1513332069 @default.
• W2149361608 cites W1536270671 @default.
• W2149361608 cites W1541767983 @default.
• W2149361608 cites W1594480768 @default.
• W2149361608 cites W1823556928 @default.
• W2149361608 cites W1944706232 @default.
• W2149361608 cites W1967409098 @default.
• W2149361608 cites W1972059142 @default.
• W2149361608 cites W1978118910 @default.
• W2149361608 cites W1988630292 @default.
• W2149361608 cites W1990383114 @default.
• W2149361608 cites W1990453950 @default.
• W2149361608 cites W2003144438 @default.
• W2149361608 cites W2004831316 @default.
• W2149361608 cites W2006481713 @default.
• W2149361608 cites W2009966494 @default.
• W2149361608 cites W2010356367 @default.
• W2149361608 cites W2013691712 @default.
• W2149361608 cites W2014808835 @default.
• W2149361608 cites W2015292449 @default.
• W2149361608 cites W2020153916 @default.
• W2149361608 cites W2020807193 @default.
• W2149361608 cites W2024291208 @default.
• W2149361608 cites W2026190471 @default.
• W2149361608 cites W2028231353 @default.
• W2149361608 cites W2028407739 @default.
• W2149361608 cites W2036662864 @default.
• W2149361608 cites W2036792999 @default.
• W2149361608 cites W2038407153 @default.
• W2149361608 cites W2043609023 @default.
• W2149361608 cites W2051895548 @default.
• W2149361608 cites W2055043387 @default.
• W2149361608 cites W2056076486 @default.
• W2149361608 cites W2061833373 @default.
• W2149361608 cites W2068018119 @default.
• W2149361608 cites W2072814963 @default.
• W2149361608 cites W2079061800 @default.
• W2149361608 cites W2085277871 @default.
• W2149361608 cites W2090297991 @default.
• W2149361608 cites W2091555639 @default.
• W2149361608 cites W2108067237 @default.
• W2149361608 cites W2110668908 @default.
• W2149361608 cites W2117019496 @default.
• W2149361608 cites W2122674287 @default.
• W2149361608 cites W2122675082 @default.
• W2149361608 cites W2123375807 @default.
• W2149361608 cites W2128329041 @default.
• W2149361608 cites W2129448726 @default.
• W2149361608 cites W2131724426 @default.
• W2149361608 cites W2136134567 @default.
• W2149361608 cites W2142628689 @default.
• W2149361608 cites W2148604640 @default.
• W2149361608 cites W2154933629 @default.
• W2149361608 cites W2155479906 @default.
• W2149361608 cites W2158714788 @default.
• W2149361608 cites W2159482845 @default.
• W2149361608 cites W2160008147 @default.
• W2149361608 cites W2164718466 @default.
• W2149361608 cites W2166575747 @default.
• W2149361608 cites W2166745327 @default.
• W2149361608 cites W217834111 @default.
• W2149361608 cites W2311085715 @default.
• W2149361608 cites W2573642578 @default.
• W2149361608 hasPublicationYear "1999" @default.
• W2149361608 type Work @default.
• W2149361608 sameAs 2149361608 @default.
• W2149361608 citedByCount "0" @default.
• W2149361608 crossrefType "journal-article" @default.
• W2149361608 hasAuthorship W2149361608A5042321575 @default.
• W2149361608 hasAuthorship W2149361608A5077758303 @default.
• W2149361608 hasConcept C104317684 @default.
• W2149361608 hasConcept C14036430 @default.
• W2149361608 hasConcept C181199279 @default.
• W2149361608 hasConcept C192772702 @default.
• W2149361608 hasConcept C207060522 @default.
• W2149361608 hasConcept C2986374874 @default.
• W2149361608 hasConcept C47701112 @default.
• W2149361608 hasConcept C55493867 @default.
• W2149361608 hasConcept C70721500 @default.
• W2149361608 hasConcept C78458016 @default.
• W2149361608 hasConcept C86803240 @default.
• W2149361608 hasConceptScore W2149361608C104317684 @default.
• W2149361608 hasConceptScore W2149361608C14036430 @default.
• W2149361608 hasConceptScore W2149361608C181199279 @default.
• W2149361608 hasConceptScore W2149361608C192772702 @default.
• W2149361608 hasConceptScore W2149361608C207060522 @default.
• W2149361608 hasConceptScore W2149361608C2986374874 @default.
• W2149361608 hasConceptScore W2149361608C47701112 @default.
• W2149361608 hasConceptScore W2149361608C55493867 @default.
• W2149361608 hasConceptScore W2149361608C70721500 @default.
• W2149361608 hasConceptScore W2149361608C78458016 @default.

• next