Matches in SemOpenAlex for { <https://semopenalex.org/work/W2889244223> ?p ?o ?g. }
Showing items 1 to 84 of
84
with 100 items per page.
- W2889244223 abstract "Abstract Motivation Direct-coupling analysis (DCA) for studying the coevolution of residues in proteins has been widely used to predict the three-dimensional structure of a protein from its sequence. Current algorithms for DCA, although efficient, have a high computational cost of determining Direct Information (DI) values for large proteins or domains. In this paper, we present RADI (Reduced Alphabet Direct Information), a variation of the original DCA algorithm that simplifies the computation of DI values by grouping physicochemically equivalent residues. Results We have compared the first top ranking 40 pairs of DI values and their closest paired contact in 3D. The ranking is also compared with results obtained using a similar but faster approach based on Mutual Information (MI). When we simplify the number of symbols used to describe a protein sequence to 9, RADI achieves similar results as the original DCA (i.e. with the classical alphabet of 21 symbols), while reducing the computation time around 30-fold on large proteins (with length around 1000 residues) and with higher accuracy than predictions based on MI. Interestingly, the simplification produced by grouping amino acids into only two groups (polar and non-polar) is still representative of the physicochemical nature that characterizes the protein structure, having a relevant and useful predictive value, while the computation time is reduced between 100 and 2500-fold. Availability RADI is available at https://github.com/structuralbioinformatics/RADI Contact baldo.oliva@upf.edu Supplementary information Supplementary data is available in the git repository." @default.
- W2889244223 created "2018-09-07" @default.
- W2889244223 creator A5001918915 @default.
- W2889244223 creator A5017470726 @default.
- W2889244223 creator A5031422458 @default.
- W2889244223 creator A5048998113 @default.
- W2889244223 creator A5065435409 @default.
- W2889244223 creator A5082536350 @default.
- W2889244223 creator A5090989775 @default.
- W2889244223 date "2018-09-03" @default.
- W2889244223 modified "2023-10-03" @default.
- W2889244223 title "RADI (Reduced Alphabet Direct Information): Improving execution time for direct-coupling analysis" @default.
- W2889244223 cites W1895528264 @default.
- W2889244223 cites W2008545402 @default.
- W2889244223 cites W2048154580 @default.
- W2889244223 cites W2051545676 @default.
- W2889244223 cites W2061042699 @default.
- W2889244223 cites W2100301244 @default.
- W2889244223 cites W2137566700 @default.
- W2889244223 cites W2139447922 @default.
- W2889244223 cites W2146891463 @default.
- W2889244223 cites W2544136853 @default.
- W2889244223 cites W2950954328 @default.
- W2889244223 cites W3101667854 @default.
- W2889244223 cites W4235787599 @default.
- W2889244223 doi "https://doi.org/10.1101/406603" @default.
- W2889244223 hasPublicationYear "2018" @default.
- W2889244223 type Work @default.
- W2889244223 sameAs 2889244223 @default.
- W2889244223 citedByCount "0" @default.
- W2889244223 crossrefType "posted-content" @default.
- W2889244223 hasAuthorship W2889244223A5001918915 @default.
- W2889244223 hasAuthorship W2889244223A5017470726 @default.
- W2889244223 hasAuthorship W2889244223A5031422458 @default.
- W2889244223 hasAuthorship W2889244223A5048998113 @default.
- W2889244223 hasAuthorship W2889244223A5065435409 @default.
- W2889244223 hasAuthorship W2889244223A5082536350 @default.
- W2889244223 hasAuthorship W2889244223A5090989775 @default.
- W2889244223 hasBestOaLocation W28892442231 @default.
- W2889244223 hasConcept C112876837 @default.
- W2889244223 hasConcept C11413529 @default.
- W2889244223 hasConcept C121332964 @default.
- W2889244223 hasConcept C1276947 @default.
- W2889244223 hasConcept C138885662 @default.
- W2889244223 hasConcept C154945302 @default.
- W2889244223 hasConcept C185592680 @default.
- W2889244223 hasConcept C189430467 @default.
- W2889244223 hasConcept C2778112365 @default.
- W2889244223 hasConcept C29705727 @default.
- W2889244223 hasConcept C41008148 @default.
- W2889244223 hasConcept C41895202 @default.
- W2889244223 hasConcept C45374587 @default.
- W2889244223 hasConcept C55493867 @default.
- W2889244223 hasConceptScore W2889244223C112876837 @default.
- W2889244223 hasConceptScore W2889244223C11413529 @default.
- W2889244223 hasConceptScore W2889244223C121332964 @default.
- W2889244223 hasConceptScore W2889244223C1276947 @default.
- W2889244223 hasConceptScore W2889244223C138885662 @default.
- W2889244223 hasConceptScore W2889244223C154945302 @default.
- W2889244223 hasConceptScore W2889244223C185592680 @default.
- W2889244223 hasConceptScore W2889244223C189430467 @default.
- W2889244223 hasConceptScore W2889244223C2778112365 @default.
- W2889244223 hasConceptScore W2889244223C29705727 @default.
- W2889244223 hasConceptScore W2889244223C41008148 @default.
- W2889244223 hasConceptScore W2889244223C41895202 @default.
- W2889244223 hasConceptScore W2889244223C45374587 @default.
- W2889244223 hasConceptScore W2889244223C55493867 @default.
- W2889244223 hasLocation W28892442231 @default.
- W2889244223 hasOpenAccess W2889244223 @default.
- W2889244223 hasPrimaryLocation W28892442231 @default.
- W2889244223 hasRelatedWork W1635337451 @default.
- W2889244223 hasRelatedWork W1975616635 @default.
- W2889244223 hasRelatedWork W2083319603 @default.
- W2889244223 hasRelatedWork W2120958014 @default.
- W2889244223 hasRelatedWork W2129645087 @default.
- W2889244223 hasRelatedWork W2138279922 @default.
- W2889244223 hasRelatedWork W2171178771 @default.
- W2889244223 hasRelatedWork W2348501199 @default.
- W2889244223 hasRelatedWork W2354062721 @default.
- W2889244223 hasRelatedWork W2748952813 @default.
- W2889244223 isParatext "false" @default.
- W2889244223 isRetracted "false" @default.
- W2889244223 magId "2889244223" @default.
- W2889244223 workType "article" @default.