2011
Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions
Bhardwaj N, Abyzov A, Clarke D, Shou C, Gerstein MB. Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions. Protein Science 2011, 20: 1745-1754. PMID: 21826754, PMCID: PMC3218368, DOI: 10.1002/pro.710.Peer-Reviewed Original ResearchMeSH KeywordsComputational BiologyDatabases, ProteinModels, MolecularProtein BindingProtein Interaction MappingProteinsSoftwareConceptsMulti-interface hubsMolecular networksConformational changesInteraction networksTransient interactionsStructural interaction networksProtein interaction networksClassification of proteinsDynamic conformational changesProtein structural featuresSmall conformational changesTransient associationGene expressionMore plasticityProtein motionsStructural databankProteinAlternate conformationDifferent mechanismsDrastic structural changesDomainInteraction
2009
RigidFinder: A fast and sensitive method to detect rigid blocks in large macromolecular complexes
Abyzov A, Bjornson R, Felipe M, Gerstein M. RigidFinder: A fast and sensitive method to detect rigid blocks in large macromolecular complexes. Proteins Structure Function And Bioinformatics 2009, 78: 309-324. PMID: 19705487, DOI: 10.1002/prot.22544.Peer-Reviewed Original ResearchConceptsLarge macromolecular complexesMacromolecular complexesLarge-scale conformational changesRNA polymerase IIT7 RNA polymeraseMultiple polypeptide chainsPolymerase IIRNA polymeraseDistance conservationPhosphate dikinaseDifferent conformationsInter-residue distancesLarge complexesConformational changesPolypeptide chainDomain motionPartial refoldingFurther distinguishing featureConformationStructure determinationComplexesDikinaseSensitive identificationGroELIdentification
2007
A comprehensive analysis of non-sequential alignments between all protein structures
Abyzov A, Ilyin V. A comprehensive analysis of non-sequential alignments between all protein structures. BMC Molecular And Cell Biology 2007, 7: 78. PMID: 18005453, PMCID: PMC2213659, DOI: 10.1186/1472-6807-7-78.Peer-Reviewed Original Research
2006
TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method
Leslin C, Abyzov A, Ilyin V. TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. Nucleic Acids Research 2006, 35: d317-d321. PMID: 17065464, PMCID: PMC1635338, DOI: 10.1093/nar/gkl809.Peer-Reviewed Original Research
2005
Friend, an integrated analytical front-end application for bioinformatics
Abyzov A, Errami M, Leslin C, Ilyin V. Friend, an integrated analytical front-end application for bioinformatics. Bioinformatics 2005, 21: 3677-3678. PMID: 16076889, DOI: 10.1093/bioinformatics/bti602.Peer-Reviewed Original ResearchConceptsSpecific interaction motifsProtein-DNA interactionsSequences of proteinsProtein folding studiesSequence-structure relationshipFunctional annotationInteraction motifsPhylogeny analysisDNA/RNAProtein modelingSequence alignmentFolding studiesRemote sequencesProteinStructural alignmentStructure databaseProgramming experienceBioinformatics applicationsSequenceCommand line interfaceExtensive GUIRNABioinformaticsFront-end applicationsMotif