Matches in SemOpenAlex for { <https://semopenalex.org/work/W2103295418> ?p ?o ?g. }
Showing items 1 to 94 of
94
with 100 items per page.
- W2103295418 abstract "Many of the nominally single-stranded hairpin, internal, and junction ldquolooprdquo regions of RNA secondary structures, in fact, form uniquely folded 3D motifs. These elements are largely structured by non-Watson-Crick basepairs. Many 3D motifs are recurrent, meaning they occur in different RNAs. Recurrent motifs have the same 3D structure but not necessarily the same sequence. We describe a methodology for identifying the sequence variability of a given recurrent RNA internal loop that can be generalized to hairpin and junction loops. Since the database of RNA 3D structures now contains a significant number of biologically active, structured RNAs, including ribosomal RNAs, ribozymes, and riboswitches, we can directly observe some of the sequence variability for recurrent motifs in x-ray crystal structures. We use our search program, FR3D, to search the 3D structure database for geometrically similar motif instances that share the same spatial pattern of basepairs. We apply our analysis of RNA basepair isostericity and occurrence frequencies to suggest likely basepair substitutions. We use the IsoDiscrepancy Index (IDI), which we recently introduced to quantify basepair isostericities, to derive 4x4 IDI Tables for each base combination in each basepair family. We illustrate how these tables can be applied to predict the most likely base substitutions that occur in a 3D motif. By comparing observed motif instances, we also determine the most likely locations of inserted (bulged) nucleotides. We compare the predictions from these considerations to observed variability in multiple sequence alignments of the motif." @default.
- W2103295418 created "2016-06-24" @default.
- W2103295418 creator A5020058613 @default.
- W2103295418 creator A5060535917 @default.
- W2103295418 creator A5069434073 @default.
- W2103295418 creator A5079806827 @default.
- W2103295418 date "2009-06-01" @default.
- W2103295418 modified "2023-10-03" @default.
- W2103295418 title "Understanding Sequence Variability of RNA Motifs Using Geometric Search and IsoDiscrepancy Matrices" @default.
- W2103295418 cites W1487900381 @default.
- W2103295418 cites W1982680051 @default.
- W2103295418 cites W1983534198 @default.
- W2103295418 cites W2019039775 @default.
- W2103295418 cites W2044247083 @default.
- W2103295418 cites W2053202362 @default.
- W2103295418 cites W2055688390 @default.
- W2103295418 cites W2089729507 @default.
- W2103295418 cites W2102304447 @default.
- W2103295418 cites W2106478835 @default.
- W2103295418 cites W2106769579 @default.
- W2103295418 cites W2119966574 @default.
- W2103295418 cites W2120339119 @default.
- W2103295418 cites W2126333637 @default.
- W2103295418 cites W2128599049 @default.
- W2103295418 cites W2141157874 @default.
- W2103295418 cites W2143733126 @default.
- W2103295418 cites W2166458835 @default.
- W2103295418 doi "https://doi.org/10.1109/occbio.2009.15" @default.
- W2103295418 hasPublicationYear "2009" @default.
- W2103295418 type Work @default.
- W2103295418 sameAs 2103295418 @default.
- W2103295418 citedByCount "2" @default.
- W2103295418 countsByYear W21032954182012 @default.
- W2103295418 countsByYear W21032954182013 @default.
- W2103295418 crossrefType "proceedings-article" @default.
- W2103295418 hasAuthorship W2103295418A5020058613 @default.
- W2103295418 hasAuthorship W2103295418A5060535917 @default.
- W2103295418 hasAuthorship W2103295418A5069434073 @default.
- W2103295418 hasAuthorship W2103295418A5079806827 @default.
- W2103295418 hasConcept C104317684 @default.
- W2103295418 hasConcept C117745874 @default.
- W2103295418 hasConcept C121332964 @default.
- W2103295418 hasConcept C126142528 @default.
- W2103295418 hasConcept C132677234 @default.
- W2103295418 hasConcept C185581394 @default.
- W2103295418 hasConcept C24890656 @default.
- W2103295418 hasConcept C2778112365 @default.
- W2103295418 hasConcept C32276052 @default.
- W2103295418 hasConcept C54355233 @default.
- W2103295418 hasConcept C552990157 @default.
- W2103295418 hasConcept C55493867 @default.
- W2103295418 hasConcept C62614982 @default.
- W2103295418 hasConcept C67705224 @default.
- W2103295418 hasConcept C67905577 @default.
- W2103295418 hasConcept C70721500 @default.
- W2103295418 hasConcept C76346623 @default.
- W2103295418 hasConcept C85468374 @default.
- W2103295418 hasConcept C86803240 @default.
- W2103295418 hasConceptScore W2103295418C104317684 @default.
- W2103295418 hasConceptScore W2103295418C117745874 @default.
- W2103295418 hasConceptScore W2103295418C121332964 @default.
- W2103295418 hasConceptScore W2103295418C126142528 @default.
- W2103295418 hasConceptScore W2103295418C132677234 @default.
- W2103295418 hasConceptScore W2103295418C185581394 @default.
- W2103295418 hasConceptScore W2103295418C24890656 @default.
- W2103295418 hasConceptScore W2103295418C2778112365 @default.
- W2103295418 hasConceptScore W2103295418C32276052 @default.
- W2103295418 hasConceptScore W2103295418C54355233 @default.
- W2103295418 hasConceptScore W2103295418C552990157 @default.
- W2103295418 hasConceptScore W2103295418C55493867 @default.
- W2103295418 hasConceptScore W2103295418C62614982 @default.
- W2103295418 hasConceptScore W2103295418C67705224 @default.
- W2103295418 hasConceptScore W2103295418C67905577 @default.
- W2103295418 hasConceptScore W2103295418C70721500 @default.
- W2103295418 hasConceptScore W2103295418C76346623 @default.
- W2103295418 hasConceptScore W2103295418C85468374 @default.
- W2103295418 hasConceptScore W2103295418C86803240 @default.
- W2103295418 hasLocation W21032954181 @default.
- W2103295418 hasOpenAccess W2103295418 @default.
- W2103295418 hasPrimaryLocation W21032954181 @default.
- W2103295418 hasRelatedWork W1999096372 @default.
- W2103295418 hasRelatedWork W2043225576 @default.
- W2103295418 hasRelatedWork W2103295418 @default.
- W2103295418 hasRelatedWork W2105070391 @default.
- W2103295418 hasRelatedWork W2125473480 @default.
- W2103295418 hasRelatedWork W2127270490 @default.
- W2103295418 hasRelatedWork W2518104501 @default.
- W2103295418 hasRelatedWork W4237472082 @default.
- W2103295418 hasRelatedWork W4386776060 @default.
- W2103295418 hasRelatedWork W85512932 @default.
- W2103295418 isParatext "false" @default.
- W2103295418 isRetracted "false" @default.
- W2103295418 magId "2103295418" @default.
- W2103295418 workType "article" @default.