2022
US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes
Zhang C, Shine M, Pyle AM, Zhang Y. US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes. Nature Methods 2022, 19: 1109-1115. PMID: 36038728, DOI: 10.1038/s41592-022-01585-1.Peer-Reviewed Original ResearchConceptsStructure comparisonStructural biology studiesStructure alignmentDNA dockingMacromolecular complexesBiology studiesMultiple structure alignmentNucleic acidsDifferent moleculesRNAProteinFundamental importanceDNAComplex structureDockingUniversal protocolAlignmentExtensive optimizationFunctionComplexes
2021
Discovery of highly reactive self-splicing group II introns within the mitochondrial genomes of human pathogenic fungi
Liu T, Pyle AM. Discovery of highly reactive self-splicing group II introns within the mitochondrial genomes of human pathogenic fungi. Nucleic Acids Research 2021, 49: 12422-12432. PMID: 34850132, PMCID: PMC8643640, DOI: 10.1093/nar/gkab1077.Peer-Reviewed Original ResearchConceptsGroup II intronsSelf-splicing group II intronsPathogenic fungiDrug targetsAntifungal drug targetsSelf-splicing intronsHuman pathogenic fungiMitochondrial genomeNear-physiological conditionsPromising drug targetProtein cofactorsStriking diversitySequence dataIntronsFungal pathogensInformatics searchBioinformatics workflowsFungiDimorphic fungusStructural signaturesPathogensGenomeCofactorDiversityTarget
2004
The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery
Wadley LM, Pyle AM. The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery. Nucleic Acids Research 2004, 32: 6650-6659. PMID: 15608296, PMCID: PMC545444, DOI: 10.1093/nar/gkh1002.Peer-Reviewed Original ResearchPrediction of functional tertiary interactions and intermolecular interfaces from primary sequence data
Pang PS, Jankowsky E, Wadley LM, Pyle AM. Prediction of functional tertiary interactions and intermolecular interfaces from primary sequence data. Journal Of Experimental Zoology Part B Molecular And Developmental Evolution 2004, 304B: 50-63. PMID: 15595717, DOI: 10.1002/jez.b.21024.Peer-Reviewed Original ResearchConceptsRNA-protein complexesPattern of conservationProtein-protein interactionsPrimary sequence dataRNA-proteinDifferent organismsSequence dataSequence informationIntermolecular interfaceEnergetic couplingTertiary interactionsMacromolecular interactionsRNAsGenesImportant intramolecular interactionsProteinSequenceIntramolecular interactionsRNAOrganismsSpeciesInteractionMutationsNumber of predictionsConservation
2003
RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space
Duarte CM, Wadley LM, Pyle AM. RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space. Nucleic Acids Research 2003, 31: 4755-4761. PMID: 12907716, PMCID: PMC169959, DOI: 10.1093/nar/gkg682.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsBase SequenceNucleic Acid ConformationRNARNA, MessengerRNA, RibosomalSoftwareConceptsRNA structureRepertoire of RNANovel RNA structuresNew RNA structuresStructural genomicsRNA functionRNA conformational spaceRibosomal subunitRNA researchRNA moleculesRNA motifsRNA structure comparisonMotif searchTertiary structureConformational changesStructure comparisonNew motifMotifReduced representationConformational spaceMacromolecular structureFuture adaptationGenomicsMajor regionsSubunits