简介：Thereisalargegapbetweenthenumberofmembraneprotein(MP)sequencesandthatoftheirdecoded3Dstructures,especiallyhigh-resolutionstructures,duetodifficultiesincrystalpreparationofMPs.However,detailedknowledgeofthe3DstructureisrequiredforthefundamentalunderstandingofthefunctionofanMPandtheinteractionsbetweentheproteinanditsinhibitorsoractivators.Inthispaper,somecomputationalapproachesthathavebeenusedtopredictMPstructuresarediscussedandcompared.

简介：TheCoronaviridaefamilyischaracterizedbyanucleocapsidthatiscomposedofthegenomeRNAmoleculeincombinationwiththenucleoprotein(Nprotein)withinavirion.ThemoststrikingphysiochemicalfeatureoftheNproteinofSARS-CoVisthatitisatypicalbasicproteinwithahighpredictedpIandhighhydrophilicity,whichisconsistentwithitsfunctionofbindingtotheribophosphatebackboneoftheRNAmolecule.ThepredictedhighextentofphosphorylationoftheNproteinonmultiplecandidatephosphorylationsitesdemonstratesthatitwouldberelatedtoimportantfunctions,suchasRNA-bindingandlocalizationtothenucleolusofhostcells.SubsequentstudyshowsthatthereisanSR-richregionintheNproteinandthisregionmightbeinvolvedintheprotein-proteininteraction.TheabundantantigenicsitespredictedintheNprotein,aswellasexperimentalevidencewithsynthesizedpolypeptides,indicatethattheNproteinisoneofthemajorantigensoftheSARS-CoV.Comparedwithotherviralstructuralproteins,thelowvariationrateoftheNproteinwithregardstoitssizesuggestsitsimportancetothesurvivalofthevirus.

简介：象从应用Biosys-tems的AB1700站台那样的新奇微数组技术在信号答应重要增加为微弱地表示的抄本的动态范围和更高的敏感。我们把AB1700数据的一个代表性的集合与同样代表性的AffymetrixHG-U133A数据集作比较。AB1700设计扩大信号在由一个数量级的更低的界限的动态察觉范围。这些高敏感的数据的日志正常信号分发侧面需要被二独立分布表示。另外的秒分发盖住将用Affymetrix技术变未被发现的那些抄本。在AB1700数据的信号依赖者变化分发是信号紧张的重要功能，用合成功能可记述。这些高敏感的transcriptome侧面的急速地不同的结构要求改编或甚至标准微数组分析方法的重新开发。基于统计性质，我们为为如此的开发是必要的AB1700数据导出一个信号变化分发模型。有趣地，在AB1700数据观察的双木头正常分发反映抄写开始的二根本上不同的生物学的机制。

简介：在这篇论文，我们与单体的二种学习一个离开格子蛋白质AB模型，恐水病、吸水、在场一个启发式的伪物理的算法。由精心地在物理世界上模仿光滑的固体的运动，首先，我们为给定的单体链发现低精力的符合构造。随后的离开陷井策略然后被建议被触发一为一种粘住的状况的jump以便从本地最小出来。算法与一些13-55单体为所有序列在三维的AB模型被测试了。在几种情况中，我们更新通常认为的地面状态精力价值。数字结果证明建议方法为发现蛋白质的扎根的状态是很有希望的。

简介：Predictingprotein-codinggenesstillremainsasignificantchallenge.Althoughavarietyofcomputationalprogramsthatusecommonlymachinelearningmethodshaveemerged,theaccuracyofpredictionsremainsalowlevelwhenimplementinginlargegenomicsequences.Moreover,computationalgenefindinginnewlyse-quencedgenomesisespeciallyadifficulttaskduetotheabsenceofatrainingsetofabundantvalidatedgenes.Herewepresentanewgene-findingprogram,SCGPred,toimprovetheaccuracyofpredictionbycombiningmultiplesourcesofevidence.SCGPredcanperformbothsupervisedmethodinpreviouslywell-studiedgenomesandunsupervisedoneinnovelgenomes.BytestingwithdatasetscomposedoflargeDNAsequencesfromhumanandanovelgenomeofUstilagomaydi,SCG-Predgainsasignificantimprovementincomparisontothepopularabinitiogenepredictors.WealsodemonstratethatSCGPredcansignificantlyimprovepredic-tioninnovelgenomesbycombiningseveralforeigngenefinderswithsimilarityalignments,whichissuperiortootherunsupervisedmethods.Therefore,SCG-Predcanserveasanalternativegene-findingtoolfornewlysequencedeukaryoticgenomes.Theprogramisfreelyavailableathttp://bio.scu.edu.cn/SCGPred/.

简介：Inourpreviousstudies,DAZAP2geneexpressionwasdown-regulatedinuntreatedpatientsofmultiplemyeloma(MM).ForbetterstudyingthestructureandfunctionofDAZAP2,afull-lengthCdnawasisolatedfrommononuclearcellsofanormalhumanbonemarrow,sequencedanddepositedtoGenbank(AY430097).ThissequencehasanidenticalORF(openreadingframe)astheNM_014764fromhumantestisandtheD31767fromhumancelllineKG-1.PhylogeneticanalysisandstructurepredictionrevealthatDAZAP2homologuesarehighlyconservedthroughoutevolutionandshareapolyprolineregionandseveralpotentialSH2/SH3bindingsites.DAZAP2occursasasingle-copygenewithafour-exonorganization.WefurthernoticedthatthefunctionalDAZAP2geneislocatedonChromosome12anditspseudogenegeneisonChromosome2withelectroniclocationofhumanchromosomeinGenbank,thoughnogeneticabnormalitiesofMMhavebeenreportedonChromosome12.TheORFofhumanDAZAP2encodesa17-kDaprotein,whichishighlysimilartomousePrtb.TheDAZAP2proteinismainlylocalizedincytoplasmwithadiscretepatternofpunctuateddistribution.DAZAP2mayassociatewithcarcinogenesisofMMandparticipateinyet-to-beidentifiedsignalingpathwaystoregulateproliferationanddifferentiationofplasmacells.

简介：陷阱，SLD5的heterotetramer，PSF1，PSF2，和PSF3蛋白质，一个新兴的染色质因素被认出涉及开始和DNA复制的延伸步。尽管酵母和Xenopus陷阱基因很好被记录，他们在更高的优核质的orthologous基因充分没被描绘。在这研究，我们报导genomic结构和哺乳动物的陷阱基因的transcriptional规定。浆液刺激在人的房间增加了GINSmRNA层次。用通常认为的陷阱倡导者序列的记者基因试金表明哺乳动物的陷阱的表示被17beta-Estradiol-stimulated雌激素受体高山调整哈，并且人的PSF3充当对抄写因素E2F1应答的基因。这研究的目标是介绍当前的数据以便在哺乳动物的房间在陷阱基因规定和函数的领域里鼓励进一步的工作。

简介：Inthepost-genomicera,variouscomputationalmethodsthatpredictprotein-proteininteractionsatthegenomelevelareavailable;however,eachmethodhasitsownadvantagesanddisadvantages,resultinginfalsepredictions.Herewedevel-opedauniqueintegratedapproachtoidentifyinteractingpartner(s)ofSemaphorin5A(SEMA5A),beginningwithsevenproteinssharingsimilarligandinteractingresiduesasputativebindingpartners.ThemethodsincludeDwyerandRoot-Bernstein/Dillontheoriesofproteinevolution,hydropathiccomplementarityofproteinstructure,patternofproteinfunctionsamongmolecules,informationondomain-domaininteractions,co-expressionofgenesandproteinevolution.AmongthesetofsevenproteinsselectedasputativeSEMA5Ainteractingpartners,wefoundthefunctionsofPlexinB3andNeuropilin-2tobeassociatedwithSEMA5A.WemodeledthesemaphorindomainstructureofPlexinB3andfoundthatitsharessimilaritywithSEMA5A.Moreover,avirtualexpressiondatabasesearchandRT-PCRanalysisshowedco-expressionofSEMA5AandPlexinB3andtheseproteinswerefoundtohaveco-evolved.Inaddition,weconfirmedtheinterac-tionofSEMA5AwithPlexinB3inco-immunoprecipitationstudies.Overall,thesestudiesdemonstratethatanintegratedmethodofpredictioncanbeusedatthegenomelevelfordiscoveringmanyunknownproteinbindingpartnerswithknownligandbindingdomains.

简介：TheR(replicase)proteinistheuniquelydefinednon-structuralprotein(NSP)responsibleforRNAreplication,mutationrateorfidelity,regulationoftranscrip-tionincoronavirusesandmanyotherssRNAviruses.Basedonourcompletegenomesequencesoffourisolates(BJ01-BJ04)ofSARS-CoVfromBeijing,China,weanalyzedthestructureandpredictedfunctionsoftheRproteinincomparisonwith13otherisolatesofSARS-CoVand6othercoronaviruses.TheentireORF(open-readingframe)encodesfortwomajorenzymeactivities,RNA-dependentRNApolymerase(RdRp)andproteinaseactivities.TheRpolyproteinunder-goesacomplexproteolyticprocesstoproduce15function-relatedpeptides.Ahydrophobicdomain(HOD)andahydrophilicdomain(HID)arenewlyidentifiedwithinNSP1.ThesubstitutionrateoftheRproteinisclosetotheaverageoftheSARS-CoVgenome.ThefunctionaldomainsinallNSPsoftheRproteingivedifferentphylogeneticresultsthatsuggesttheirdifferentmutationrateunderselectivepressure.ElevenhighlyconservedregionsinRdRpandtwelvecleavagesitesby3CLP(chymotrypsin-likeprotein)havebeenidentifiedaspotentialdrugtargets.Findingssuggestthatitispossibletoobtaininformationaboutthephy-logenyofSARS-CoV,aswellaspotentialtoolsfordrugdesign,genotypinganddiagnosticsofSARS.