FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2000236879> ?p ?o ?g. }

• W2000236879 endingPage "e9391" @default.
• W2000236879 startingPage "e9391" @default.
• W2000236879 abstract "Vastly divergent sequences populate a majority of protein folds. In the quest to identify features that are conserved within protein domains belonging to the same fold, we set out to examine the entire protein universe on a fold-by-fold basis. We report that the atomic interaction network in the solvent-unexposed core of protein domains are fold-conserved, extraordinary sequence divergence notwithstanding. Further, we find that this feature, termed protein core atomic interaction network (or PCAIN) is significantly distinguishable across different folds, thus appearing to be “signature” of a domain's native fold. As part of this study, we computed the PCAINs for 8698 representative protein domains from families across the 1018 known protein folds to construct our seed database and an automated framework was developed for PCAIN-based characterization of the protein fold universe. A test set of randomly selected domains that are not in the seed database was classified with over 97% accuracy, independent of sequence divergence. As an application of this novel fold signature, a PCAIN-based scoring scheme was developed for comparative (homology-based) structure prediction, with 1–2 angstroms (mean 1.61A) Cα RMSD generally observed between computed structures and reference crystal structures. Our results are consistent across the full spectrum of test domains including those from recent CASP experiments and most notably in the ‘twilight’ and ‘midnight’ zones wherein <30% and <10% target-template sequence identity prevails (mean twilight RMSD of 1.69A). We further demonstrate the utility of the PCAIN protocol to derive biological insight into protein structure-function relationships, by modeling the structure of the YopM effector novel E3 ligase (NEL) domain from plague-causative bacterium Yersinia Pestis and discussing its implications for host adaptive and innate immune modulation by the pathogen. Considering the several high-throughput, sequence-identity-independent applications demonstrated in this work, we suggest that the PCAIN is a fundamental fold feature that could be a valuable addition to the arsenal of protein modeling and analysis tools." @default.
• W2000236879 created "2016-06-24" @default.
• W2000236879 creator A5001410017 @default.
• W2000236879 creator A5002241220 @default.
• W2000236879 creator A5015523412 @default.
• W2000236879 creator A5065374721 @default.
• W2000236879 creator A5091684658 @default.
• W2000236879 date "2010-02-23" @default.
• W2000236879 modified "2023-10-03" @default.
• W2000236879 title "Atomic Interaction Networks in the Core of Protein Domains and Their Native Folds" @default.
• W2000236879 cites W1546896179 @default.
• W2000236879 cites W157808733 @default.
• W2000236879 cites W1585607520 @default.
• W2000236879 cites W1966711452 @default.
• W2000236879 cites W1969007008 @default.
• W2000236879 cites W1969268163 @default.
• W2000236879 cites W1973459793 @default.
• W2000236879 cites W1973897761 @default.
• W2000236879 cites W1975252459 @default.
• W2000236879 cites W1980777635 @default.
• W2000236879 cites W1984932018 @default.
• W2000236879 cites W1985818354 @default.
• W2000236879 cites W1994983243 @default.
• W2000236879 cites W1999177257 @default.
• W2000236879 cites W2008708467 @default.
• W2000236879 cites W2011570309 @default.
• W2000236879 cites W2015470526 @default.
• W2000236879 cites W2016225859 @default.
• W2000236879 cites W2023790301 @default.
• W2000236879 cites W2030775654 @default.
• W2000236879 cites W2042036635 @default.
• W2000236879 cites W2044228129 @default.
• W2000236879 cites W2045777307 @default.
• W2000236879 cites W2049902088 @default.
• W2000236879 cites W2050330741 @default.
• W2000236879 cites W2050625197 @default.
• W2000236879 cites W2054243594 @default.
• W2000236879 cites W2065127848 @default.
• W2000236879 cites W2076917731 @default.
• W2000236879 cites W2078889580 @default.
• W2000236879 cites W2080333909 @default.
• W2000236879 cites W2085142174 @default.
• W2000236879 cites W2091221943 @default.
• W2000236879 cites W2096413602 @default.
• W2000236879 cites W2101712920 @default.
• W2000236879 cites W2105765197 @default.
• W2000236879 cites W2114496049 @default.
• W2000236879 cites W2130497192 @default.
• W2000236879 cites W2132122858 @default.
• W2000236879 cites W2132868108 @default.
• W2000236879 cites W2135498219 @default.
• W2000236879 cites W2142529984 @default.
• W2000236879 cites W2144482528 @default.
• W2000236879 cites W2151693654 @default.
• W2000236879 cites W2153077385 @default.
• W2000236879 cites W2153187042 @default.
• W2000236879 cites W2156408001 @default.
• W2000236879 cites W2163333444 @default.
• W2000236879 cites W2167420772 @default.
• W2000236879 cites W2472076038 @default.
• W2000236879 cites W2011495938 @default.
• W2000236879 doi "https://doi.org/10.1371/journal.pone.0009391" @default.
• W2000236879 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2826414" @default.
• W2000236879 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/20186337" @default.
• W2000236879 hasPublicationYear "2010" @default.
• W2000236879 type Work @default.
• W2000236879 sameAs 2000236879 @default.
• W2000236879 citedByCount "39" @default.
• W2000236879 countsByYear W20002368792012 @default.
• W2000236879 countsByYear W20002368792013 @default.
• W2000236879 countsByYear W20002368792014 @default.
• W2000236879 countsByYear W20002368792015 @default.
• W2000236879 countsByYear W20002368792016 @default.
• W2000236879 countsByYear W20002368792018 @default.
• W2000236879 countsByYear W20002368792019 @default.
• W2000236879 countsByYear W20002368792022 @default.
• W2000236879 crossrefType "journal-article" @default.
• W2000236879 hasAuthorship W2000236879A5001410017 @default.
• W2000236879 hasAuthorship W2000236879A5002241220 @default.
• W2000236879 hasAuthorship W2000236879A5015523412 @default.
• W2000236879 hasAuthorship W2000236879A5065374721 @default.
• W2000236879 hasAuthorship W2000236879A5091684658 @default.
• W2000236879 hasBestOaLocation W20002368791 @default.
• W2000236879 hasConcept C10010492 @default.
• W2000236879 hasConcept C104317684 @default.
• W2000236879 hasConcept C121332964 @default.
• W2000236879 hasConcept C144292202 @default.
• W2000236879 hasConcept C167625842 @default.
• W2000236879 hasConcept C18051474 @default.
• W2000236879 hasConcept C204328495 @default.
• W2000236879 hasConcept C47701112 @default.
• W2000236879 hasConcept C54355233 @default.
• W2000236879 hasConcept C55493867 @default.
• W2000236879 hasConcept C70721500 @default.
• W2000236879 hasConcept C78458016 @default.
• W2000236879 hasConcept C86803240 @default.
• W2000236879 hasConceptScore W2000236879C10010492 @default.
• W2000236879 hasConceptScore W2000236879C104317684 @default.

• next