{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,4]],"date-time":"2024-08-04T11:21:49Z","timestamp":1722770509190},"reference-count":45,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2008,7,4]],"date-time":"2008-07-04T00:00:00Z","timestamp":1215129600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000105","type":"journal-article","created":{"date-parts":[[2008,7,3]],"date-time":"2008-07-03T17:31:32Z","timestamp":1215106292000},"page":"e1000105","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":15,"title":["Local Function Conservation in Sequence and Structure Space"],"prefix":"10.1371","volume":"4","author":[{"given":"Nils","family":"Weinhold","sequence":"first","affiliation":[]},{"given":"Oliver","family":"Sander","sequence":"additional","affiliation":[]},{"given":"Francisco S.","family":"Domingues","sequence":"additional","affiliation":[]},{"given":"Thomas","family":"Lengauer","sequence":"additional","affiliation":[]},{"given":"Ingolf","family":"Sommer","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2008,7,4]]},"reference":[{"key":"ref1","first-page":"25","article-title":"Gene ontology: tool for the unification of biology.","volume":"25","author":"M Ashburner","year":"2000","journal-title":"The Gene Ontology Consortium. Nat Genet"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1006\/jmbi.2001.4513","article-title":"Evolution of function in protein superfamilies, from a structural perspective.","volume":"307","author":"AE Todd","year":"2001","journal-title":"J Mol Biol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1016\/j.jmb.2003.08.057","article-title":"How well is enzyme function conserved as a function of pairwise sequence identity?","volume":"333","author":"W Tian","year":"2003","journal-title":"J Mol Biol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1016\/S0022-2836(02)00016-5","article-title":"Enzyme function less conserved than anticipated.","volume":"318","author":"B Rost","year":"2002","journal-title":"J Mol Biol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"2637","DOI":"10.1007\/s00018-003-3114-8","article-title":"Automatic prediction of protein function.","volume":"60","author":"B Rost","year":"2003","journal-title":"Cell Mol Life Sci"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1017\/S0033583503003901","article-title":"Prediction of protein function from protein sequence and structure.","volume":"36","author":"JC Whisstock","year":"2003","journal-title":"Q Rev Biophys"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1186\/1471-2105-5-178","article-title":"GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes.","volume":"5","author":"DMA Martin","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"3674","DOI":"10.1093\/bioinformatics\/bti610","article-title":"Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.","volume":"21","author":"A Conesa","year":"2005","journal-title":"Bioinformatics"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1550","DOI":"10.1110\/ps.062153506","article-title":"Enhanced automated function prediction using distantly related sequences and contextual association by PFP.","volume":"15","author":"T Hawkins","year":"2006","journal-title":"Protein Sci"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"e45","DOI":"10.1371\/journal.pcbi.0010045","article-title":"Protein molecular function prediction by bayesian phylogenomics.","volume":"1","author":"BE Engelhardt","year":"2005","journal-title":"PLoS Comput Biol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1093\/bioinformatics\/18.1.92","article-title":"Automated ortholog inference from phylogenetic trees and calculation of orthology reliability.","volume":"18","author":"CEV Storm","year":"2002","journal-title":"Bioinformatics"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1093\/nar\/29.1.202","article-title":"The EMOTIF database.","volume":"29","author":"JY Huang","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"D227","DOI":"10.1093\/nar\/gkj063","article-title":"The PROSITE database.","volume":"34","author":"N Hulo","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"3341","DOI":"10.1093\/nar\/gkg506","article-title":"Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures.","volume":"31","author":"A Stark","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"D281","DOI":"10.1093\/nar\/gkj057","article-title":"Gene3D: modelling protein structure, function and evolution.","volume":"34","author":"C Yeats","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"2969","DOI":"10.1093\/bioinformatics\/bti471","article-title":"FSSA: a novel method for identifying functional signatures from structural alignments.","volume":"21","author":"K Wang","year":"2005","journal-title":"Bioinformatics"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"14754","DOI":"10.1073\/pnas.0404569101","article-title":"Automated prediction of protein function and detection of functional sites from structure.","volume":"101","author":"F Pazos","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref18","first-page":"1211","article-title":"Inferring protein function from protein structure.","author":"FS Domingues","year":"2007"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1016\/j.sbi.2005.04.003","article-title":"Predicting protein function from sequence and structural data.","volume":"15","author":"JD Watson","year":"2005","journal-title":"Curr Opin Struct Biol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1093\/bioinformatics\/btg036","article-title":"Prediction of human protein function according to gene ontology categories.","volume":"19","author":"LJ Jensen","year":"2003","journal-title":"Bioinformatics"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"D358","DOI":"10.1093\/nar\/gkl825","article-title":"STRING 7\u2013recent developments in the integration and prediction of protein interactions.","volume":"35","author":"C von Mering","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"896","DOI":"10.1101\/gr.440803","article-title":"Predicting gene function from patterns of annotation.","volume":"13","author":"OD King","year":"2003","journal-title":"Genome Res"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/j.str.2004.10.015","article-title":"Inference of protein function from protein structure.","volume":"13","author":"D Pal","year":"2005","journal-title":"Structure"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"W89","DOI":"10.1093\/nar\/gki414","article-title":"ProFunc: a server for predicting protein function from 3D structure.","volume":"33","author":"RA Laskowski","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"W379","DOI":"10.1093\/nar\/gkl045","article-title":"JAFA: a protein function annotation meta-server.","volume":"34","author":"I Friedberg","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1093\/bib\/bbl004","article-title":"Automated protein function prediction\u2013the genomic challenge.","volume":"7","author":"I Friedberg","year":"2006","journal-title":"Brief Bioinform"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1186\/1471-2105-8-294","article-title":"Quantitative sequence-function relationships in proteins based on gene ontology.","volume":"8","author":"V Sangar","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1186\/1471-2164-8-222","article-title":"Quantitative assessment of relationship between sequence similarity and function similarity.","volume":"8","author":"T Joshi","year":"2007","journal-title":"BMC Genomics"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1186\/1471-2105-8-170","article-title":"Estimating the annotation error rate of curated GO database sequence annotations.","volume":"8","author":"CE Jones","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1006\/jmbi.1999.2661","article-title":"The relationship between protein structure and function: a comprehensive survey with application to the yeast genome.","volume":"288","author":"H Hegyi","year":"1999","journal-title":"J Mol Biol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1006\/jmbi.2000.3550","article-title":"Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.","volume":"297","author":"CA Wilson","year":"2000","journal-title":"J Mol Biol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"D189","DOI":"10.1093\/nar\/gkh034","article-title":"The ASTRAL compendium in 2004.","volume":"32","author":"JM Chandonia","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1101\/gr.461403","article-title":"The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.","volume":"13","author":"E Camon","year":"2003","journal-title":"Genome Res"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"D262","DOI":"10.1093\/nar\/gkh021","article-title":"The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.","volume":"32","author":"E Camon","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref35","first-page":"252","article-title":"Profile-profile alignment: a powerful tool for protein structure prediction.","author":"N von \u00d6hsen","year":"2003","journal-title":"Pac Symp Biocomput"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1093\/protein\/11.9.739","article-title":"Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.","volume":"11","author":"IN Shindyalov","year":"1998","journal-title":"Protein Eng"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"2302","DOI":"10.1093\/nar\/gki524","article-title":"TM-align: a protein structure alignment algorithm based on the TM-score.","volume":"33","author":"Y Zhang","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref38","first-page":"D190","article-title":"The universal protein resource (UniProt).","volume":"36","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1194","DOI":"10.1016\/j.jinorgbio.2004.05.002","article-title":"Structure and direct electrochemistry of cytochrome p450 from the thermoacidophilic crenarchaeon, sulfolobus tokodaii strain 7.","volume":"98","author":"Y Oku","year":"2004","journal-title":"J Inorg Biochem"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"D247","DOI":"10.1093\/nar\/gkj149","article-title":"Pfam: clans, web tools and services.","volume":"34","author":"RD Finn","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1110\/ps.041229405","article-title":"Crystal structure of a predicted phosphoribosyltransferase (tt1426) from thermus thermophilus hb8 at 2.01 a resolution.","volume":"14","author":"M Kukimoto-Niino","year":"2005","journal-title":"Protein Sci"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1093\/nar\/28.1.254","article-title":"The ASTRAL compendium for protein structure and sequence analysis.","volume":"28","author":"SE Brenner","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"4297","DOI":"10.1093\/bioinformatics\/bti694","article-title":"Mapping PDB chains to UniProtKB entries.","volume":"21","author":"ACR Martin","year":"2005","journal-title":"Bioinformatics"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1007\/BF02289694","article-title":"Non metric multidimensional scaling: a numerical method.","volume":"29","author":"JB Kruskal","year":"1964","journal-title":"Psychometrika"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"4125","DOI":"10.1021\/bi962640d","article-title":"Crystal structure of Escherichia coli xanthine phosphoribosyltransferase.","volume":"36","author":"S Vos","year":"1997","journal-title":"Biochemistry"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000105","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,22]],"date-time":"2018-10-22T10:00:55Z","timestamp":1540202455000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000105"}},"subtitle":[],"editor":[{"given":"Burkhard","family":"Rost","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2008,7,4]]},"references-count":45,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2008,7,4]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000105","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,7,4]]}}}