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 optimizationFunctionComplexesCSSR: assignment of secondary structure to coarse‐grained RNA tertiary structures
Zhang C, Pyle AM. CSSR: assignment of secondary structure to coarse‐grained RNA tertiary structures. Acta Crystallographica Section D, Structural Biology 2022, 78: 466-471. PMID: 35362469, PMCID: PMC8972804, DOI: 10.1107/s2059798322001292.Peer-Reviewed Original Research
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 Research
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