{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T08:44:37Z","timestamp":1778057077551,"version":"3.51.4"},"reference-count":96,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2010,11,24]],"date-time":"2010-11-24T00:00:00Z","timestamp":1290556800000},"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.1001017","type":"journal-article","created":{"date-parts":[[2010,11,24]],"date-time":"2010-11-24T20:35:15Z","timestamp":1290630915000},"page":"e1001017","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":41,"title":["Sequence Motifs in MADS Transcription Factors Responsible for Specificity and Diversification of Protein-Protein Interaction"],"prefix":"10.1371","volume":"6","author":[{"given":"Aalt D. J.","family":"van Dijk","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giuseppa","family":"Morabito","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martijn","family":"Fiers","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roeland C. H. J.","family":"van Ham","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gerco C.","family":"Angenent","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard G. H.","family":"Immink","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2010,11,24]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1038\/nature03991","article-title":"Evolutionary information for specifying a protein fold.","volume":"437","author":"M Socolich","year":"2005","journal-title":"Nature"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1868","DOI":"10.1126\/science.1113801","article-title":"Toward high-resolution de novo structure prediction for small proteins.","volume":"309","author":"P Bradley","year":"2005","journal-title":"Science"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"1415","DOI":"10.1073\/pnas.0812510106","article-title":"Generalized ensemble methods for de novo structure prediction.","volume":"106","author":"A Shmygelska","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"3734","DOI":"10.1073\/pnas.0811363106","article-title":"Mimicking the folding pathway to improve homology-free protein structure prediction.","volume":"106","author":"J DeBartolo","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1038\/nature07885","article-title":"Design of protein-interaction specificity gives selective bZIP-binding peptides.","volume":"458","author":"G Grigoryan","year":"2009","journal-title":"Nature"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1016\/j.cell.2008.04.040","article-title":"Rewiring the specificity of two-component signal transduction systems.","volume":"133","author":"JM Skerker","year":"2008","journal-title":"Cell"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1038\/nature03990","article-title":"Natural-like function in artificial WW domains.","volume":"437","author":"WP Russ","year":"2005","journal-title":"Nature"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1038\/nature04177","article-title":"A quantitative protein interaction network for the ErbB receptors using protein microarrays.","volume":"439","author":"RB Jones","year":"2006","journal-title":"Nature"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1371\/journal.pbio.0020014","article-title":"Protein interaction networks by proteome peptide scanning.","volume":"2","author":"C Landgraf","year":"2004","journal-title":"Plos Biology"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1038\/nbt.1489","article-title":"Predicting PDZ domain-peptide interactions from primary sequences.","volume":"26","author":"JR Chen","year":"2008","journal-title":"Nat Biotechnol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1038\/nsmb.1670","article-title":"Following evolutionary paths to protein-protein interactions with high affinity and selectivity.","volume":"16","author":"KB Levin","year":"2009","journal-title":"Nat Struct Mol Biol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"e1000052","DOI":"10.1371\/journal.pcbi.1000052","article-title":"Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm.","volume":"4","author":"IE Sanchez","year":"2008","journal-title":"PLoS Comput Biol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"4629","DOI":"10.1093\/nar\/gkp394","article-title":"Using genome-wide measurements for computational prediction of SH2-peptide interactions.","volume":"37","author":"Z Wunderlich","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"i274","DOI":"10.1093\/bioinformatics\/bth922","article-title":"Predicting protein-peptide interactions via a network-based motif sampler.","volume":"20","author":"DJ Reiss","year":"2004","journal-title":"Bioinformatics"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"2333","DOI":"10.1093\/bioinformatics\/btl403","article-title":"A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity.","volume":"22","author":"E Ferraro","year":"2006","journal-title":"Bioinformatics"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1093\/bioinformatics\/bti804","article-title":"A regularized discriminative model for the prediction of protein-peptide interactions.","volume":"22","author":"WP Lehrach","year":"2006","journal-title":"Bioinformatics"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"1169","DOI":"10.1371\/journal.pcbi.0030119","article-title":"Protein-protein interaction hotspots carved into sequences.","volume":"3","author":"Y Ofran","year":"2007","journal-title":"Plos Computational Biology"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"R171","DOI":"10.1093\/hmg\/ddi335","article-title":"Interactome: gateway into systems biology.","volume":"14","author":"ME Cusick","year":"2005","journal-title":"Hum Mol Genet"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1016\/S1360-1385(02)02343-9","article-title":"Transcription factors do it together: the hows and whys of studying protein-protein interactions.","volume":"7","author":"RGH Immink","year":"2002","journal-title":"Trends Plant Sci"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"e42","DOI":"10.1371\/journal.pcbi.0030042","article-title":"Deciphering Protein-Protein Interactions. Part I. Experimental Techniques and Databases.","volume":"3","author":"BA Shoemaker","year":"2007","journal-title":"PLoS Comput Biol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/35048107","article-title":"Protein interaction maps for model organisms.","volume":"2","author":"AJM Walhout","year":"2001","journal-title":"Nat Rev Mol Cell Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"13292","DOI":"10.1073\/pnas.0801207105","article-title":"Built-in loops allow versatility in domain-domain interactions: Lessons from self-interacting domains.","volume":"105","author":"E Akiva","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1016\/j.tplants.2003.09.006","article-title":"And then there were many: MADS goes genomic.","volume":"8","author":"S De Bodt","year":"2003","journal-title":"Trends Plant Sci"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1538","DOI":"10.1105\/tpc.011544","article-title":"Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: New openings to the MADS world.","volume":"15","author":"L Parenicova","year":"2003","journal-title":"Plant Cell"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1424","DOI":"10.1105\/tpc.105.031831","article-title":"Comprehensive interaction map of the Arabidopsis MADS box transcription factors.","volume":"17","author":"S de Folter","year":"2005","journal-title":"Plant Cell"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/j.semcdb.2009.10.004","article-title":"The \u2018ABC\u2019 of MADS domain protein behaviour and interactions.","volume":"21","author":"RGH Immink","year":"2010","journal-title":"Semin Cell Dev Biol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"4330","DOI":"10.1002\/j.1460-2075.1996.tb00807.x","article-title":"Multiple interactions amongst floral homeotic MADS box proteins.","volume":"15","author":"B Davies","year":"1996","journal-title":"Embo Journal"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"4063","DOI":"10.1073\/pnas.93.9.4063","article-title":"Mapping the protein regions responsible for the functional specificities of the Arabidopsis MADS domain organ-identity proteins.","volume":"93","author":"BA Krizek","year":"1996","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"4793","DOI":"10.1073\/pnas.93.10.4793","article-title":"Dimerization specificity of Arabidopsis MADS domain homeotic proteins APETALA1, APETALA3, PISTILLATA, and AGAMOUS.","volume":"93","author":"JL Riechmann","year":"1996","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1038\/353031a0","article-title":"The war of the whorls: genetic interactions controlling flower development.","volume":"353","author":"ES Coen","year":"1991","journal-title":"Nature"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1016\/j.pbi.2003.11.003","article-title":"Conservation and diversity in flower land.","volume":"7","author":"S Ferrario","year":"2004","journal-title":"Curr Opin Plant Biol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.semcdb.2009.10.005","article-title":"Floral organ identity: 20 years of ABCs.","volume":"21","author":"B Causier","year":"2010","journal-title":"Semin Cell Dev Biol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1038\/35054172","article-title":"Plant biology - Floral quartets.","volume":"409","author":"G Theissen","year":"2001","journal-title":"Nature"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1038\/35056041","article-title":"Function and evolution of the plant MADS-box gene family.","volume":"2","author":"M Ng","year":"2001","journal-title":"Nat Rev Genet"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1016\/j.pbi.2009.07.006","article-title":"Just say no: floral repressors help Arabidopsis bide the time.","volume":"12","author":"L Yant","year":"2009","journal-title":"Curr Opin Plant Biol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1016\/j.tibs.2004.09.006","article-title":"The power of two: protein dimerization in biology.","volume":"29","author":"NJ Marianayagam","year":"2004","journal-title":"Trends Biochem Sci"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1146\/annurev.immunol.16.1.569","article-title":"Dimerization as a regulatory mechanism in signal transduction.","volume":"16","author":"JD Klemm","year":"1998","journal-title":"Annu Rev Immunol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1016\/j.tibs.2008.02.002","article-title":"Choose your partners: dimerization in eukaryotic transcription factors.","volume":"33","author":"GD Amoutzias","year":"2008","journal-title":"Trends Biochem Sci"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1016\/j.tree.2005.07.008","article-title":"Genome duplication and the origin of angiosperms.","volume":"20","author":"S De Bodt","year":"2005","journal-title":"Trends Ecol Evol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"2416","DOI":"10.1073\/pnas.042677699","article-title":"Analysis of MADS box protein-protein interactions in living plant cells.","volume":"99","author":"RGH Immink","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"914","DOI":"10.1105\/tpc.010280","article-title":"The MADS box gene FBP2 is required for SEPALLATA function in petunia.","volume":"15","author":"S Ferrario","year":"2003","journal-title":"Plant Cell"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1105\/tpc.019166","article-title":"The duplicated B-class heterodimer model: Whorl-specific effects and complex genetic interactions in Petunia hybrida flower development.","volume":"16","author":"M Vandenbussche","year":"2004","journal-title":"Plant Cell"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"4157","DOI":"10.1242\/dev.013136","article-title":"Functional analyses of genetic pathways controlling petal specification in poppy.","volume":"134","author":"S Drea","year":"2007","journal-title":"Development"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1093\/bioinformatics\/btm539","article-title":"Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control.","volume":"24","author":"ADJ van Dijk","year":"2008","journal-title":"Bioinformatics"},{"key":"ref45","article-title":"The \u2018ABC\u2019 of MADS domain protein behaviour and interactions.","volume":"In press","author":"RGH Immink","year":"2009","journal-title":"Semin Cell Dev Biol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1038\/nature01555","article-title":"Sequence-specific recruitment of transcriptional co-repressor Cabin1 by myocyte enhancer factor-2.","volume":"422","author":"AD Han","year":"2003","journal-title":"Nature"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1101\/gad.5.3.484","article-title":"Agl1-Agl6, an Arabidopsis Gene Family with Similarity to Floral Homeotic and Transcription Factor Genes.","volume":"5","author":"H Ma","year":"1991","journal-title":"Genes Dev"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/j.gene.2004.12.014","article-title":"MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants.","volume":"347","author":"K Kaufmann","year":"2005","journal-title":"Gene"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1002\/j.1460-2075.1992.tb05048.x","article-title":"Characterization of the Antirrhinum Floral Homeotic Mads-Box Gene Deficiens - Evidence for DNA-Binding and Autoregulation of Its Persistent Expression Throughout Flower Development.","volume":"11","author":"Z Schwarzsommer","year":"1992","journal-title":"Embo Journal"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"4076","DOI":"10.1128\/MCB.15.8.4076","article-title":"DNA-Binding Specificity Determinants in Mads-Box Transcription Factors.","volume":"15","author":"SJ Nurrish","year":"1995","journal-title":"Mol Cell Biol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1046\/j.0960-7412.2003.01473.x","article-title":"The K domain mediates heterodimerization of the Arabidopsis floral organ identity proteins, APETALA3 and PISTILLATA.","volume":"33","author":"YZ Yang","year":"2003","journal-title":"Plant J"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1007\/s11103-004-0416-7","article-title":"Defining subdomains of the K domain important for protein-protein interactions of plant MADS proteins.","volume":"55","author":"YZ Yang","year":"2004","journal-title":"Plant Mol Biol"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1126\/science.7824951","article-title":"Molecular-Basis of the Cauliflower Phenotype in Arabidopsis.","volume":"267","author":"SA Kempin","year":"1995","journal-title":"Science"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1046\/j.1365-313x.2000.00682.x","article-title":"Molecular cloning of SVP: a negative regulator of the floral transition in Arabidopsis.","volume":"21","author":"U Hartmann","year":"2000","journal-title":"Plant J"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.devcel.2008.05.002","article-title":"A repressor complex governs the integration of flowering signals in Arabidopsis.","volume":"15","author":"D Li","year":"2008","journal-title":"Developmental Cell"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1105\/tpc.009506","article-title":"Analysis of the Arabidopsis MADS AFFECTING FLOWERING gene family: MAF2 prevents vernalization by short periods of cold.","volume":"15","author":"OJ Ratcliffe","year":"2003","journal-title":"Plant Cell"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1186\/gb-2009-10-5-107","article-title":"The 1001 Genomes Project for Arabidopsis thaliana.","volume":"10","author":"D Weigel","year":"2009","journal-title":"Genome Biology"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"2603","DOI":"10.1105\/tpc.015123","article-title":"MADS-box protein complexes control carpel and ovule development in Arabidopsis.","volume":"15","author":"R Favaro","year":"2003","journal-title":"Plant Cell"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"1935","DOI":"10.1016\/j.cub.2004.10.028","article-title":"The SEP4 gene of Arabidopsis thaliana functions in floral organ and meristem identity.","volume":"14","author":"G Ditta","year":"2004","journal-title":"Curr Biol"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"3419","DOI":"10.1093\/jxb\/erl144","article-title":"Protein interactions of MADS box transcription factors involved in flowering in Lolium perenne.","volume":"57","author":"S Ciannamea","year":"2006","journal-title":"J Exp Bot"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"7096","DOI":"10.1073\/pnas.100101997","article-title":"A ligand-reversible dimerization system for controlling protein-protein interactions.","volume":"97","author":"CT Rollins","year":"2000","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"7748","DOI":"10.1073\/pnas.0500932102","article-title":"A single amino acid converts a repressor to an activator of flowering.","volume":"102","author":"Y Hanzawa","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"R192","DOI":"10.1186\/gb-2007-8-9-r192","article-title":"InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.","volume":"8","author":"H Wang","year":"2007","journal-title":"Genome Biol"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"2122","DOI":"10.1371\/journal.pcbi.0030211","article-title":"Detecting coevolution in and among protein domains.","volume":"3","author":"CH Yeang","year":"2007","journal-title":"Plos Computational Biology"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1038\/msb4100203","article-title":"Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method.","volume":"4","author":"L Burger","year":"2008","journal-title":"Molecular Systems Biology"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1073\/pnas.0805923106","article-title":"Identification of direct residue contacts in protein-protein interaction by message passing.","volume":"106","author":"M Weigt","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1101\/gr.1774904","article-title":"Annotation transfer between genomes: Protein-protein interologs and protein-DNA regulogs.","volume":"14","author":"HY Yu","year":"2004","journal-title":"Genome Res"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"698","DOI":"10.1371\/journal.pcbi.0020079","article-title":"Protein-protein interactions more conserved within species than across species.","volume":"2","author":"S Mika","year":"2006","journal-title":"Plos Computational Biology"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1016\/S1367-5931(00)00206-4","article-title":"Combinatorial alanine-scanning.","volume":"5","author":"KL Morrison","year":"2001","journal-title":"Curr Opin Chem Biol"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1038\/nrg2499","article-title":"The evolution of hierarchical gene regulatory networks.","volume":"10","author":"DH Erwin","year":"2009","journal-title":"Nat Rev Genet"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"766","DOI":"10.1038\/35008089","article-title":"SHATTERPROOF MADS-box genes control seed dispersal in Arabidopsis.","volume":"404","author":"SJ Liljegren","year":"2000","journal-title":"Nature"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1038\/35012103","article-title":"B and C floral organ identity functions require SEPALLATA MADS-box genes.","volume":"405","author":"S Pelaz","year":"2000","journal-title":"Nature"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1111\/j.1365-313X.2007.03105.x","article-title":"The MADS domain factors AGL15 and AGL18 act redundantly as repressors of the floral transition in Arabidopsis.","volume":"50","author":"BJ Adamczyk","year":"2007","journal-title":"Plant J"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"5370","DOI":"10.1093\/emboj\/18.19.5370","article-title":"Ternary complex formation between the MADS-box proteins SQUAMOSA, DEFICIENS and GLOBOSA is involved in the control of floral architecture in Antirrhinum majus.","volume":"18","author":"M Egea-Cortines","year":"1999","journal-title":"Embo Journal"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/35054083","article-title":"Complexes of MADS-box proteins are sufficient to convert leaves into floral organs.","volume":"409","author":"T Honma","year":"2001","journal-title":"Nature"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"R24","DOI":"10.1186\/gb-2009-10-2-r24","article-title":"SEPALLATA3: the \u2018glue\u2019 for MADS box transcription factor complex formation.","volume":"10","author":"RGH Immink","year":"2009","journal-title":"Genome Biology"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"3134","DOI":"10.1093\/nar\/24.16.3134","article-title":"DNA-binding properties of Arabidopsis MADS domain homeotic proteins APETALA1, APETALA3, PISTILLATA and AGAMOUS.","volume":"24","author":"JL Riechmann","year":"1996","journal-title":"Nucleic Acids Res"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"854","DOI":"10.1371\/journal.pbio.1000090","article-title":"Target Genes of the MADS Transcription Factor SEPALLATA3: Integration of Developmental and Hormonal Pathways in the Arabidopsis Flower.","volume":"7","author":"K Kaufmann","year":"2009","journal-title":"Plos Biology"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1186\/1471-2105-7-502","article-title":"A correlated motif approach for finding short linear motifs from protein interaction networks.","volume":"7","author":"SH Tan","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1023\/A:1010933404324","article-title":"Random forests.","volume":"45","author":"L Breiman","year":"2001","journal-title":"Machine Learning"},{"key":"ref81","article-title":"Gene selection and classification of microarray data using random forest.","volume":"7","author":"R Diaz-Uriate","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1002\/(SICI)1521-3773(19990115)38:1\/2<236::AID-ANIE236>3.0.CO;2-M","article-title":"Peptide folding: When simulation meets experiment.","volume":"38","author":"X Daura","year":"1999","journal-title":"Angewandte Chemie-International Edition"},{"issue":"Pt B","key":"ref83","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/S0076-6879(02)50957-5","article-title":"Transformation of yeast by lithium acetate\/single-stranded carrier DNA\/polyethylene glycol method.","volume":"350","author":"RD Gietz","year":"2002","journal-title":"Guide to Yeast Genetics and Molecular and Cell Biology"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1006\/jmbi.1993.1626","article-title":"Comparative Protein Modeling by Satisfaction of Spatial Restraints.","volume":"234","author":"A Sali","year":"1993","journal-title":"J Mol Biol"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1006\/jmbi.2000.3568","article-title":"Crystal structure of MEF2A core bound to DNA at 1.5 angstrom resolution.","volume":"297","author":"E Santelli","year":"2000","journal-title":"J Mol Biol"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"-","DOI":"10.1186\/1471-2105-9-278","article-title":"Scipio: Using protein sequences to determine the precise exon\/intron structures of genes and their orthologs in closely related species.","volume":"9","author":"O Keller","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"-","DOI":"10.1186\/1471-2164-8-242","article-title":"MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress.","volume":"8","author":"R Arora","year":"2007","journal-title":"BMC Genomics"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1093\/molbev\/msk016","article-title":"Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting.","volume":"23","author":"S De Bodt","year":"2006","journal-title":"Mol Biol Evol"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"e1326","DOI":"10.1371\/journal.pone.0001326","article-title":"A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety.","volume":"2","author":"R Velasco","year":"2007","journal-title":"PLoS ONE"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1038\/nature06856","article-title":"The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).","volume":"452","author":"R Ming","year":"2008","journal-title":"Nature"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1038\/nature07723","article-title":"The Sorghum bicolor genome and the diversification of grasses.","volume":"457","author":"AH Paterson","year":"2009","journal-title":"Nature"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1093\/bioinformatics\/14.9.755","article-title":"Profile hidden Markov models.","volume":"14","author":"SR Eddy","year":"1998","journal-title":"Bioinformatics"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"D211","DOI":"10.1093\/nar\/gkp985","article-title":"The Pfam protein families database.","volume":"38","author":"RD Finn","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput.","volume":"32","author":"RC Edgar","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1016\/S1055-7903(03)00207-0","article-title":"The major clades of MADS-box genes and their role in the development and evolution of flowering plants.","volume":"29","author":"A Becker","year":"2003","journal-title":"Mol Phylogenet Evol"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1534\/genetics.105.053249","article-title":"A novel method for detecting intramolecular coevolution: Adding a further dimension to selective constraints analyses.","volume":"173","author":"MA Fares","year":"2006","journal-title":"Genetics"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1001017","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,6,6]],"date-time":"2019-06-06T14:31:13Z","timestamp":1559831473000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1001017"}},"subtitle":[],"editor":[{"given":"Christos","family":"Ouzounis","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2010,11,24]]},"references-count":96,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2010,11,24]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1001017","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,11,24]]}}}