Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models 英文参考文献.docVIP

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Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models 英文参考文献.doc

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Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models 英文参考文献

FunctionalCoverageoftheHumanGenome byExistingStructures,StructuralGenomics Targets,andHomologyModels Lei Xie, Philip E.Bourne* SanDiegoSupercomputerCenterandDepartmentofPharmacology,UniversityofCalifornia,SanDiego,California,UnitedStatesofAmerica The bias in protein structure and function space resulting from experimental limitations and targeting of particular functional classes of proteins by structural biologists has long been recognized, but never continuously quantified. UsingtheEnzymeCommissionandtheGeneOntologyclassificationsasareferenceframe,andintegratingstructure datafromtheProteinDataBank(PDB),targetsequencesfromthestructuralgenomicsprojects,structurehomology derivedfromtheSUPERFAMILYdatabase,andgenomeannotationsfromEnsemblandNCBI,weprovideaquantified view, both at the domain and whole-protein levels, of the current and projected coverage of protein structure and function space relative to the human genome. Protein structures currently provide at least one domain that covers 37%ofthefunctionalclassesidentifiedinthegenome;wholestructurecoverageexistsfor25%ofthegenome.Ifall thestructuralgenomicstargetsweresolved(twicethecurrentnumberofstructuresinthePDB),itisestimatedthat structuresofonedomainwouldcover69%ofthefunctionalclassesidentifiedandcompletestructurecoveragewould be44%.Homologymodelsfromexistingexperimentalstructuresextendthe37%coverageto56%ofthegenomeas singledomainsand25%to31%forcompletestructures.Coveragefromhomologymodelsisnotevenlydistributedby protein family, reflecting differing degrees of sequence and structure divergence within families. While these data provide coverage, conversely, they also systematically highlight functional classes of proteins for which structures shouldbedetermined.Currentkeyfunctionalfamilieswithoutstructurerepresentationarehighlightedhere;updated informationonthe‘‘mostwantedlist’’thatshouldbesolvedisavailableonaweeklybasisfromhttp://function.rcsb. org:8080/pdb/function_distribution/index.html. Citation:XieL,BourneP