FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2154954910> ?p ?o ?g. }

• W2154954910 endingPage "1003" @default.
• W2154954910 startingPage "996" @default.
• W2154954910 abstract "Abstract Motivation: Helix–helix interactions play a critical role in the structure assembly, stability and function of membrane proteins. On the molecular level, the interactions are mediated by one or more residue contacts. Although previous studies focused on helix-packing patterns and sequence motifs, few of them developed methods specifically for contact prediction. Results: We present a new hierarchical framework for contact prediction, with an application in membrane proteins. The hierarchical scheme consists of two levels: in the first level, contact residues are predicted from the sequence and their pairing relationships are further predicted in the second level. Statistical analyses on contact propensities are combined with other sequence and structural information for training the support vector machine classifiers. Evaluated on 52 protein chains using leave-one-out cross validation (LOOCV) and an independent test set of 14 protein chains, the two-level approach consistently improves the conventional direct approach in prediction accuracy, with 80% reduction of input for prediction. Furthermore, the predicted contacts are then used to infer interactions between pairs of helices. When at least three predicted contacts are required for an inferred interaction, the accuracy, sensitivity and specificity are 56%, 40% and 89%, respectively. Our results demonstrate that a hierarchical framework can be applied to eliminate false positives (FP) while reducing computational complexity in predicting contacts. Together with the estimated contact propensities, this method can be used to gain insights into helix-packing in membrane proteins. Availability: http://bio-cluster.iis.sinica.edu.tw/TMhit/ Contact: tsung@iis.sinica.edu.tw Supplementary information: Supplementary data are available at Bioinformatics online." @default.
• W2154954910 created "2016-06-24" @default.
• W2154954910 creator A5002526597 @default.
• W2154954910 creator A5017920981 @default.
• W2154954910 creator A5028741023 @default.
• W2154954910 creator A5028815334 @default.
• W2154954910 creator A5075392444 @default.
• W2154954910 creator A5088763169 @default.
• W2154954910 date "2009-02-25" @default.
• W2154954910 modified "2023-09-23" @default.
• W2154954910 title "Predicting helix–helix interactions from residue contacts in membrane proteins" @default.
• W2154954910 cites W1970605146 @default.
• W2154954910 cites W1985935502 @default.
• W2154954910 cites W1986049071 @default.
• W2154954910 cites W1991921179 @default.
• W2154954910 cites W1992657771 @default.
• W2154954910 cites W1994373739 @default.
• W2154954910 cites W2012604750 @default.
• W2154954910 cites W2031368570 @default.
• W2154954910 cites W2031644342 @default.
• W2154954910 cites W2034177352 @default.
• W2154954910 cites W2050749891 @default.
• W2154954910 cites W2056402029 @default.
• W2154954910 cites W2056825408 @default.
• W2154954910 cites W2074362388 @default.
• W2154954910 cites W2074437547 @default.
• W2154954910 cites W2076444761 @default.
• W2154954910 cites W2082102819 @default.
• W2154954910 cites W2087300028 @default.
• W2154954910 cites W2097123168 @default.
• W2154954910 cites W2097980499 @default.
• W2154954910 cites W2098481780 @default.
• W2154954910 cites W2099715859 @default.
• W2154954910 cites W2100063856 @default.
• W2154954910 cites W2101466114 @default.
• W2154954910 cites W2109553965 @default.
• W2154954910 cites W2123969230 @default.
• W2154954910 cites W2130479394 @default.
• W2154954910 cites W2133657429 @default.
• W2154954910 cites W2135572502 @default.
• W2154954910 cites W2141718854 @default.
• W2154954910 cites W2141920771 @default.
• W2154954910 cites W2143814286 @default.
• W2154954910 cites W2145336405 @default.
• W2154954910 cites W2146388379 @default.
• W2154954910 cites W2155051670 @default.
• W2154954910 cites W2156125289 @default.
• W2154954910 cites W2158580600 @default.
• W2154954910 cites W2158714788 @default.
• W2154954910 cites W2160535028 @default.
• W2154954910 cites W2170907233 @default.
• W2154954910 cites W4298850410 @default.
• W2154954910 doi "https://doi.org/10.1093/bioinformatics/btp114" @default.
• W2154954910 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2666818" @default.
• W2154954910 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/19244388" @default.
• W2154954910 hasPublicationYear "2009" @default.
• W2154954910 type Work @default.
• W2154954910 sameAs 2154954910 @default.
• W2154954910 citedByCount "59" @default.
• W2154954910 countsByYear W21549549102012 @default.
• W2154954910 countsByYear W21549549102013 @default.
• W2154954910 countsByYear W21549549102014 @default.
• W2154954910 countsByYear W21549549102015 @default.
• W2154954910 countsByYear W21549549102016 @default.
• W2154954910 countsByYear W21549549102017 @default.
• W2154954910 countsByYear W21549549102018 @default.
• W2154954910 countsByYear W21549549102019 @default.
• W2154954910 countsByYear W21549549102020 @default.
• W2154954910 countsByYear W21549549102022 @default.
• W2154954910 countsByYear W21549549102023 @default.
• W2154954910 crossrefType "journal-article" @default.
• W2154954910 hasAuthorship W2154954910A5002526597 @default.
• W2154954910 hasAuthorship W2154954910A5017920981 @default.
• W2154954910 hasAuthorship W2154954910A5028741023 @default.
• W2154954910 hasAuthorship W2154954910A5028815334 @default.
• W2154954910 hasAuthorship W2154954910A5075392444 @default.
• W2154954910 hasAuthorship W2154954910A5088763169 @default.
• W2154954910 hasBestOaLocation W21549549101 @default.
• W2154954910 hasConcept C144647389 @default.
• W2154954910 hasConcept C154945302 @default.
• W2154954910 hasConcept C185592680 @default.
• W2154954910 hasConcept C186060115 @default.
• W2154954910 hasConcept C18903297 @default.
• W2154954910 hasConcept C2778112365 @default.
• W2154954910 hasConcept C2778530040 @default.
• W2154954910 hasConcept C2779965526 @default.
• W2154954910 hasConcept C41008148 @default.
• W2154954910 hasConcept C41625074 @default.
• W2154954910 hasConcept C55493867 @default.
• W2154954910 hasConcept C64869954 @default.
• W2154954910 hasConcept C70721500 @default.
• W2154954910 hasConcept C86803240 @default.
• W2154954910 hasConceptScore W2154954910C144647389 @default.
• W2154954910 hasConceptScore W2154954910C154945302 @default.
• W2154954910 hasConceptScore W2154954910C185592680 @default.
• W2154954910 hasConceptScore W2154954910C186060115 @default.
• W2154954910 hasConceptScore W2154954910C18903297 @default.
• W2154954910 hasConceptScore W2154954910C2778112365 @default.

• next