ECOD,ECOD,ECOD,ECOD,ECOD,ECOD,ECOD,ECOD,ECOD,ECOD,ECOD:,new,developments,evolutionary,classification,domains,Evolutionary,Classification,protein,Domains,,ECOD,,,http://prodata.swmed.edu/ecod,,comprehensively,classifies,protein,known,spatial,structures,maintained,Protein,Data,Bank,,PDB,,evolutionary,groups,protein,domains,ECOD,relies,combination,automatic,manual,weekly,updates,achieve,high,accuracy,coverage,short,update,cycle,ECOD,classifies,approximately,120,000,depositions,PDB,500,000,domains,?3400,homologous,groups,show,performance,weekly,update,pipeline,since,release,ECOD,,describe,improvements,ECOD,website,available,search,options,,discuss,novel,structures,homologous,groups,classified,recent,updates,Finally,,discuss,future,directions,ECOD,improvements,planned,hierarchy,update,process,©,Author,s,,2016,Published,Oxford,University,Press,behalf,Nucleic,Acids,Research.ECOD:,evolutionary,classification,protein,domains,Understanding,evolution,protein,,including,close,distant,relationships,,often,reveals,insight,structure,function,Fast,easy,access,up-to-date,information,facilitates,research,developed,hierarchical,evolutionary,classification,proteins,experimentally,determined,spatial,structures,,presented,interactive,updatable,online,database,ECOD,,Evolutionary,Classification,protein,Domains,,distinct,structural,classifications,groups,domains,primarily,evolutionary,relationships,,homology,,,rather,topology,,"fold",,distinction,highlights,cases,homology,domains,differing,topology,aid,understanding,protein,structure,evolution,ECOD,uniquely,emphasizes,distantly,related,homologs,difficult,detect,,thus,catalogs,largest,number,evolutionary,links,among,structural,domain,classifications,Placing,distant,homologs,together,underscores,ancestral,similarities,proteins,draws,attention,important,regions,sequence,structure,,well,conserved,functional,sites,ECOD,also,recognizes,closer,sequence-based,relationships,protein,domains,Currently,,approximately,100,000,protein,structures,classified,ECOD,9,000,sequence,families,clustered,close,2,000,evolutionary,groups,classification,assisted,automated,pipeline,quickly,consistently,classifies,weekly,releases,PDB,structures,allows,continual,updates,synchronization,PDB,uniquely,distinguishes,ECOD,among,protein,classifications,Finally,,present,several,case,studies,homologous,proteins,recorded,classifications,,illustrating,potential,ECOD,can,used,biological,evolutionary,studies.Manual,classification,strategies,ECOD,database,ECOD,,Evolutionary,Classification,protein,Domains,,comprehensive,up-to-date,protein,structure,classification,database,majority,new,structures,released,PDB,,Protein,Data,Bank,,week,already,close,homologs,ECOD,hierarchy,thus,can,reliably,partitioned,domains,classified,software,without,manual,intervention,However,,proteins,lack,confidently,detectable,homologs,require,careful,analysis,experts,Although,many,bioinformatics,resources,rely,expert,curation,degree,,specific,examples,curation,occurs,cases,necessary,always,described,,illustrate,manual,classification,strategy,ECOD,example,,focusing,two,major,issues,protein,classification:,domain,partitioning,relationship,homology,similarity,scores,examples,show,recently,released,manually,classified,PDB,structures,discuss,multi-domain,proteins,,discordance,sequence,structural,similarities,,difficulties,assessing,homology,scores,,integral,membrane,proteins,homologous,soluble,proteins,timely,assimilation,newly,available,structures,hierarchy,,ECOD,strives,provide,accurate,updated,view,protein,structure,world,result,combined,computational,expert-driven,analysis,©,2015,Wiley,Periodicals,,Inc.A,sequence,family,database,built,ECOD,structural,domains,Motivation:,ECOD,database,classifies,protein,domains,based,evolutionary,relationships,,considering,remote,close,homology,family,group,ECOD,provides,classification,domains,closely,related,based,sequence,similarity,Due,different,perspectives,domain,definition,,direct,application,existing,sequence,domain,databases,,Pfam,,ECOD,struggles,several,shortcomings.<br>Results:,created,multiple,sequence,alignments,profiles,ECOD,domains,help,structural,information,alignment,building,boundary,delineation,validated,alignment,quality,scoring,structure,superposition,demonstrate,comparable,curated,seed,alignments,Pfam,Comparison,Pfam,CDD,reveals,27,16%,ECOD,families,new,,also,dominated,small,families,,likely,sampling,bias,PDB,database,35,48%,families,whose,boundaries,modified,comparing,counterparts,Pfam,CDD,,respectively.<br>Availability,implementation:,new,families,now,integrated,ECOD,website,aggregate,HMMER,profile,library,alignment,available,download,ECOD,website,,http://prodata.swmed.edu/ecod,.<br>Supplementary,information:,Supplementary,data,available,Bioinformatics,online.<br>,ECOD:,new,developments,evolutionary,classification,domains,Evolutionary,Classification,protein,Domains,,ECOD,,,http://prodata.swmed.edu/ecod,,comprehensively,classifies,protein,known,spatial,structures,maintained,Protein,Data,Bank,,PDB,,evolutionary,groups,protein,domains,ECOD,relies,combination,automatic,manual,weekly,updates,achieve,high,accuracy,coverage,short,update,cycle,ECOD,classifies,approximately,120,000,depositions,PDB,500,000,domains,?3400,homologous,groups,show,performance,weekly,update,pipeline,since,release,ECOD,,describe,improvements,ECOD,website,available,search,options,,discuss,novel,structures,homologous,groups,classified,recent,updates,Finally,,discuss,future,directions,ECOD,improvements,planned,hierarchy,update,process,©,Author,s,,2016,Published,Oxford,University,Press,behalf,Nucleic,Acids,Research.ECOD:,evolutionary,classification,protein,domains,Understanding,evolution,protein,,including,close,distant,relationships,,often,reveals,insight,structure,function,Fast,easy,access,up-to-date,information,facilitates,research,developed,hierarchical,evolutionary,classification,proteins,experimentally,determined,spatial,structures,,presented,interactive,updatable,online,database,ECOD,,Evolutionary,Classification,protein,Domains,,distinct,structural,classifications,groups,domains,primarily,evolutionary,relationships,,homology,,,rather,topology,,"fold",,distinction,highlights,cases,homology,domains,differing,topology,aid,understanding,protein,structure,evolution,ECOD,uniquely,emphasizes,distantly,related,homologs,difficult,detect,,thus,catalogs,largest,number,evolutionary,links,among,structural,domain,classifications,Placing,distant,homologs,together,underscores,ancestral,similarities,proteins,draws,attention,important,regions,sequence,structure,,well,conserved,functional,sites,ECOD,also,recognizes,closer,sequence-based,relationships,protein,domains,Currently,,approximately,100,000,protein,structures,classified,ECOD,9,000,sequence,families,clustered,close,2,000,evolutionary,groups,classification,assisted,automated,pipeline,quickly,consistently,classifies,weekly,releases,PDB,structures,allows,continual,updates,synchronization,PDB,uniquely,distinguishes,ECOD,among,protein,classifications,Finally,,present,several,case,studies,homologous,proteins,recorded,classifications,,illustrating,potential,ECOD,can,used,biological,evolutionary,studies.Manual,classification,strategies,ECOD,database,ECOD,,Evolutionary,Classification,protein,Domains,,comprehensive,up-to-date,protein,structure,classification,database,majority,new,structures,released,PDB,,Protein,Data,Bank,,week,already,close,homologs,ECOD,hierarchy,thus,can,reliably,partitioned,domains,classified,software,without,manual,intervention,However,,proteins,lack,confidently,detectable,homologs,require,careful,analysis,experts,Although,many,bioinformatics,resources,rely,expert,curation,degree,,specific,examples,curation,occurs,cases,necessary,always,described,,illustrate,manual,classification,strategy,ECOD,example,,focusing,two,major,issues,protein,classification:,domain,partitioning,relationship,homology,similarity,scores,examples,show,recently,released,manually,classified,PDB,structures,discuss,multi-domain,proteins,,discordance,sequence,structural,similarities,,difficulties,assessing,homology,scores,,integral,membrane,proteins,homologous,soluble,proteins,timely,assimilation,newly,available,structures,hierarchy,,ECOD,strives,provide,accurate,updated,view,protein,structure,world,result,combined,computational,expert-driven,analysis,©,2015,Wiley,Periodicals,,Inc.A,sequence,family,database,built,ECOD,structural,domains,Motivation:,ECOD,database,classifies,protein,domains,based,evolutionary,relationships,,considering,remote,close,homology,family,group,ECOD,provides,classification,domains,closely,related,based,sequence,similarity,Due,different,perspectives,domain,definition,,direct,application,existing,sequence,domain,databases,,Pfam,,ECOD,struggles,several,shortcomings.<br>Results:,created,multiple,sequence,alignments,profiles,ECOD,domains,help,structural,information,alignment,building,boundary,delineation,validated,alignment,quality,scoring,structure,superposition,demonstrate,comparable,curated,seed,alignments,Pfam,Comparison,Pfam,CDD,reveals,27,16%,ECOD,families,new,,also,dominated,small,families,,likely,sampling,bias,PDB,database,35,48%,families,whose,boundaries,modified,comparing,counterparts,Pfam,CDD,,respectively.<br>Availability,implementation:,new,families,now,integrated,ECOD,website,aggregate,HMMER,profile,library,alignment,available,download,ECOD,website,,http://prodata.swmed.edu/ecod,.<br>Supplementary,information:,Supplementary,data,available,Bioinformatics,online.<br>