{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,8,22]],"date-time":"2023-08-22T15:13:56Z","timestamp":1692717236334},"reference-count":37,"publisher":"Springer Science and Business Media LLC","issue":"S6","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2008,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>DNA-binding proteins are of utmost importance to gene regulation. The identification of DNA-binding domains is useful for understanding the regulation mechanisms of DNA-binding proteins. In this study, we proposed a method to determine whether a domain or a protein can has DNA binding capability by considering evolutionary conservation of DNA-binding residues.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Our method achieves high precision and recall for 66 families of DNA-binding domains, with a false positive rate less than 5% for 250 non-DNA-binding proteins. In addition, experimental results show that our method is able to identify the different DNA-binding behaviors of proteins in the same SCOP family based on the use of evolutionary conservation of DNA-contact residues.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>This study shows the conservation of DNA-contact residues in DNA-binding domains. We conclude that the members in the same subfamily bind DNA specifically and the members in different subfamilies often recognize different DNA targets. Additionally, we observe the co-evolution of DNA-contact residues and interacting DNA base-pairs.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-9-s6-s3","type":"journal-article","created":{"date-parts":[[2008,5,28]],"date-time":"2008-05-28T18:15:34Z","timestamp":1211998534000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Evolutionary conservation of DNA-contact residues in DNA-binding domains"],"prefix":"10.1186","volume":"9","author":[{"given":"Yao-Lin","family":"Chang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huai-Kuang","family":"Tsai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cheng-Yan","family":"Kao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yung-Chian","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuh-Jyh","family":"Hu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinn-Moon","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,5,28]]},"reference":[{"issue":"2","key":"2614_CR1","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1016\/j.jmb.2004.01.033","volume":"337","author":"M Michael Gromiha","year":"2004","unstructured":"Michael Gromiha M, Siebers JG, Selvaraj S, Kono H, Sarai A: Intermolecular and intramolecular readout mechanisms in protein-DNA recognition. J Mol Biol 2004,337(2):285\u2013294. 10.1016\/j.jmb.2004.01.033","journal-title":"J Mol Biol"},{"issue":"4932","key":"2614_CR2","doi-asserted-by":"publisher","first-page":"911","DOI":"10.1126\/science.2683088","volume":"246","author":"CR Vinson","year":"1989","unstructured":"Vinson CR, Sigler PB, McKnight SL: Scissors-grip model for DNA recognition by a family of leucine zipper proteins. Science 1989,246(4932):911\u2013916. 10.1126\/science.2683088","journal-title":"Science"},{"issue":"6346","key":"2614_CR3","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1038\/353715a0","volume":"353","author":"SC Harrison","year":"1991","unstructured":"Harrison SC: A structural taxonomy of DNA-binding domains. Nature 1991,353(6346):715\u2013719. 10.1038\/353715a0","journal-title":"Nature"},{"issue":"1","key":"2614_CR4","doi-asserted-by":"publisher","first-page":"REVIEWS001","DOI":"10.1186\/gb-2000-1-1-reviews001","volume":"1","author":"NM Luscombe","year":"2000","unstructured":"Luscombe NM, Austin SE, Berman HM, Thornton JM: An overview of the structures of protein-DNA complexes. Genome Biol 2000,1(1):REVIEWS001. 10.1186\/gb-2000-1-1-reviews001","journal-title":"Genome Biol"},{"key":"2614_CR5","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1146\/annurev.bi.58.070189.004055","volume":"58","author":"PF Johnson","year":"1989","unstructured":"Johnson PF, McKnight SL: Eukaryotic transcriptional regulatory proteins. Annu Rev Biochem 1989, 58: 799\u2013839. 10.1146\/annurev.bi.58.070189.004055","journal-title":"Annu Rev Biochem"},{"issue":"1","key":"2614_CR6","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1016\/j.jmb.2004.05.058","volume":"341","author":"S Ahmad","year":"2004","unstructured":"Ahmad S, Sarai A: Moment-based prediction of DNA-binding proteins. J Mol Biol 2004,341(1):65\u201371. 10.1016\/j.jmb.2004.05.058","journal-title":"J Mol Biol"},{"issue":"4","key":"2614_CR7","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1093\/bioinformatics\/btg432","volume":"20","author":"S Ahmad","year":"2004","unstructured":"Ahmad S, Gromiha MM, Sarai A: Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics 2004,20(4):477\u2013486. 10.1093\/bioinformatics\/btg432","journal-title":"Bioinformatics"},{"issue":"4","key":"2614_CR8","doi-asserted-by":"publisher","first-page":"885","DOI":"10.1002\/prot.20111","volume":"55","author":"Y Tsuchiya","year":"2004","unstructured":"Tsuchiya Y, Kinoshita K, Nakamura H: Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces. Proteins 2004,55(4):885\u2013894. 10.1002\/prot.20111","journal-title":"Proteins"},{"issue":"20","key":"2614_CR9","doi-asserted-by":"publisher","first-page":"6486","DOI":"10.1093\/nar\/gki949","volume":"33","author":"N Bhardwaj","year":"2005","unstructured":"Bhardwaj N, Langlois RE, Zhao G, Lu H: Kernel-based machine learning protocol for predicting DNA-binding proteins. Nucleic Acids Res 2005,33(20):6486\u20136493. 10.1093\/nar\/gki949","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"2614_CR10","doi-asserted-by":"publisher","first-page":"1058","DOI":"10.1016\/j.febslet.2007.01.086","volume":"581","author":"N Bhardwaj","year":"2007","unstructured":"Bhardwaj N, Lu H: Residue-level prediction of DNA-binding sites and its application on DNA-binding protein predictions. FEBS Lett 2007,581(5):1058\u20131066. 10.1016\/j.febslet.2007.01.086","journal-title":"FEBS Lett"},{"issue":"2","key":"2614_CR11","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1016\/j.jtbi.2005.09.018","volume":"240","author":"X Yu","year":"2006","unstructured":"Yu X, Cao J, Cai Y, Shi T, Li Y: Predicting rRNA-, RNA-, and DNA-binding proteins from primary structure with support vector machines. J Theor Biol 2006,240(2):175\u2013184. 10.1016\/j.jtbi.2005.09.018","journal-title":"J Theor Biol"},{"issue":"3","key":"2614_CR12","doi-asserted-by":"publisher","first-page":"922","DOI":"10.1016\/j.jmb.2006.02.053","volume":"358","author":"A Szilagyi","year":"2006","unstructured":"Szilagyi A, Skolnick J: Efficient prediction of nucleic acid binding function from low-resolution protein structures. J Mol Biol 2006,358(3):922\u2013933. 10.1016\/j.jmb.2006.02.053","journal-title":"J Mol Biol"},{"key":"2614_CR13","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/1471-2105-6-33","volume":"6","author":"S Ahmad","year":"2005","unstructured":"Ahmad S, Sarai A: PSSM-based prediction of DNA binding sites in proteins. BMC Bioinformatics 2005, 6: 33. 10.1186\/1471-2105-6-33","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"2614_CR14","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1002\/prot.20977","volume":"64","author":"IB Kuznetsov","year":"2006","unstructured":"Kuznetsov IB, Gou Z, Li R, Hwang S: Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins. Proteins 2006,64(1):19\u201327. 10.1002\/prot.20977","journal-title":"Proteins"},{"issue":"5","key":"2614_CR15","doi-asserted-by":"publisher","first-page":"1465","DOI":"10.1093\/nar\/gkm008","volume":"35","author":"H Tjong","year":"2007","unstructured":"Tjong H, Zhou HX: DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Nucleic Acids Res 2007,35(5):1465\u20131477. 10.1093\/nar\/gkm008","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"2614_CR16","doi-asserted-by":"publisher","first-page":"991","DOI":"10.1016\/S0022-2836(02)00571-5","volume":"320","author":"NM Luscombe","year":"2002","unstructured":"Luscombe NM, Thornton JM: Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. J Mol Biol 2002,320(5):991\u20131009. 10.1016\/S0022-2836(02)00571-5","journal-title":"J Mol Biol"},{"issue":"4","key":"2614_CR17","doi-asserted-by":"publisher","first-page":"1065","DOI":"10.1016\/S0022-2836(03)00031-7","volume":"326","author":"EW Stawiski","year":"2003","unstructured":"Stawiski EW, Gregoret LM, Mandel-Gutfreund Y: Annotating nucleic acid-binding function based on protein structure. J Mol Biol 2003,326(4):1065\u20131079. 10.1016\/S0022-2836(03)00031-7","journal-title":"J Mol Biol"},{"issue":"22","key":"2614_CR18","doi-asserted-by":"publisher","first-page":"10915","DOI":"10.1073\/pnas.89.22.10915","volume":"89","author":"S Henikoff","year":"1992","unstructured":"Henikoff S, Henikoff JG: Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992,89(22):10915\u201310919. 10.1073\/pnas.89.22.10915","journal-title":"Proc Natl Acad Sci USA"},{"issue":"3","key":"2614_CR19","doi-asserted-by":"publisher","first-page":"522","DOI":"10.1002\/pro.5560030317","volume":"3","author":"U Hobohm","year":"1994","unstructured":"Hobohm U, Sander C: Enlarged representative set of protein structures. Protein Sci 1994,3(3):522\u2013524.","journal-title":"Protein Sci"},{"issue":"6721","key":"2614_CR20","doi-asserted-by":"publisher","first-page":"714","DOI":"10.1038\/17833","volume":"397","author":"JM Passner","year":"1999","unstructured":"Passner JM, Ryoo HD, Shen L, Mann RS, Aggarwal AK: Structure of a DNA-bound Ultrabithorax-Extradenticle homeodomain complex. Nature 1999,397(6721):714\u2013719. 10.1038\/17833","journal-title":"Nature"},{"issue":"16","key":"2614_CR21","doi-asserted-by":"publisher","first-page":"2060","DOI":"10.1101\/gad.1103303","volume":"17","author":"NA LaRonde-LeBlanc","year":"2003","unstructured":"LaRonde-LeBlanc NA, Wolberger C: Structure of HoxA9 and Pbx1 bound to DNA: Hox hexapeptide and DNA recognition anterior to posterior. Genes Dev 2003,17(16):2060\u20132072. 10.1101\/gad.1103303","journal-title":"Genes Dev"},{"issue":"4","key":"2614_CR22","doi-asserted-by":"publisher","first-page":"427","DOI":"10.1016\/S0092-8674(00)81584-6","volume":"94","author":"RN Dutnall","year":"1998","unstructured":"Dutnall RN, Tafrov ST, Sternglanz R, Ramakrishnan V: Structure of the histone acetyltransferase Hat1: a paradigm for the GCN5-related N-acetyltransferase superfamily. Cell 1998,94(4):427\u2013438. 10.1016\/S0092-8674(00)81584-6","journal-title":"Cell"},{"issue":"2","key":"2614_CR23","doi-asserted-by":"publisher","first-page":"1449","DOI":"10.1074\/jbc.M309790200","volume":"279","author":"DC Williams Jr","year":"2004","unstructured":"Williams DC Jr, Cai M, Clore GM: Molecular basis for synergistic transcriptional activation by Oct1 and Sox2 revealed from the solution structure of the 42-kDa Oct1.Sox2.Hoxb1-DNA ternary transcription factor complex. J Biol Chem 2004,279(2):1449\u20131457. 10.1074\/jbc.M309790200","journal-title":"J Biol Chem"},{"issue":"3","key":"2614_CR24","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1002\/prot.20921","volume":"64","author":"AS Konagurthu","year":"2006","unstructured":"Konagurthu AS, Whisstock JC, Stuckey PJ, Lesk AM: MUSTANG: a multiple structural alignment algorithm. Proteins 2006,64(3):559\u2013574. 10.1002\/prot.20921","journal-title":"Proteins"},{"issue":"4","key":"2614_CR25","doi-asserted-by":"publisher","first-page":"536","DOI":"10.1006\/jmbi.1995.0159","volume":"247","author":"AG Murzin","year":"1995","unstructured":"Murzin AG, Brenner SE, Hubbard T, Chothia C: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995,247(4):536\u2013540. 10.1006\/jmbi.1995.0159","journal-title":"J Mol Biol"},{"issue":"13","key":"2614_CR26","doi-asserted-by":"publisher","first-page":"2860","DOI":"10.1093\/nar\/29.13.2860","volume":"29","author":"NM Luscombe","year":"2001","unstructured":"Luscombe NM, Laskowski RA, Thornton JM: Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res 2001,29(13):2860\u20132874. 10.1093\/nar\/29.13.2860","journal-title":"Nucleic Acids Res"},{"issue":"18","key":"2614_CR27","doi-asserted-by":"publisher","first-page":"5781","DOI":"10.1093\/nar\/gki875","volume":"33","author":"AV Morozov","year":"2005","unstructured":"Morozov AV, Havranek JJ, Baker D, Siggia ED: Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res 2005,33(18):5781\u20135798. 10.1093\/nar\/gki875","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"2614_CR28","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1006\/jmbi.1993.1489","volume":"233","author":"L Holm","year":"1993","unstructured":"Holm L, Sander C: Protein structure comparison by alignment of distance matrices. J Mol Biol 1993,233(1):123\u2013138. 10.1006\/jmbi.1993.1489","journal-title":"J Mol Biol"},{"issue":"8","key":"2614_CR29","doi-asserted-by":"publisher","first-page":"2444","DOI":"10.1073\/pnas.85.8.2444","volume":"85","author":"WR Pearson","year":"1988","unstructured":"Pearson WR, Lipman DJ: Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988,85(8):2444\u20132448. 10.1073\/pnas.85.8.2444","journal-title":"Proc Natl Acad Sci USA"},{"key":"2614_CR30","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1016\/S0076-6879(96)66017-0","volume":"266","author":"WR Pearson","year":"1996","unstructured":"Pearson WR: Effective protein sequence comparison. Methods Enzymol 1996, 266: 227\u2013258.","journal-title":"Methods Enzymol"},{"key":"2614_CR31","first-page":"185","volume":"132","author":"WR Pearson","year":"2000","unstructured":"Pearson WR: Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol 2000, 132: 185\u2013219.","journal-title":"Methods Mol Biol"},{"issue":"1","key":"2614_CR32","doi-asserted-by":"publisher","first-page":"R7","DOI":"10.1016\/S0969-2126(99)80003-3","volume":"7","author":"TF Smith","year":"1999","unstructured":"Smith TF: The art of matchmaking: sequence alignment methods and their structural implications. Structure 1999,7(1):R7-R12. 10.1016\/S0969-2126(99)80003-3","journal-title":"Structure"},{"issue":"1","key":"2614_CR33","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1016\/S0167-7799(99)01398-0","volume":"18","author":"J Skolnick","year":"2000","unstructured":"Skolnick J, Fetrow JS: From genes to protein structure and function: novel applications of computational approaches in the genomic era. Trends Biotechnol 2000,18(1):34\u201339. 10.1016\/S0167-7799(99)01398-0","journal-title":"Trends Biotechnol"},{"issue":"3","key":"2614_CR34","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","volume":"48","author":"SB Needleman","year":"1970","unstructured":"Needleman SB, Wunsch CD: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970,48(3):443\u2013453. 10.1016\/0022-2836(70)90057-4","journal-title":"J Mol Biol"},{"issue":"1","key":"2614_CR35","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","volume":"147","author":"TF Smith","year":"1981","unstructured":"Smith TF, Waterman MS: Identification of common molecular subsequences. J Mol Biol 1981,147(1):195\u2013197. 10.1016\/0022-2836(81)90087-5","journal-title":"J Mol Biol"},{"issue":"10","key":"2614_CR36","doi-asserted-by":"publisher","first-page":"846","DOI":"10.1093\/bioinformatics\/14.10.846","volume":"14","author":"K Karplus","year":"1998","unstructured":"Karplus K, Barrett C, Hughey R: Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998,14(10):846\u2013856. 10.1093\/bioinformatics\/14.10.846","journal-title":"Bioinformatics"},{"issue":"3","key":"2614_CR37","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990,215(3):403\u2013410.","journal-title":"J Mol Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-S6-S3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T07:56:48Z","timestamp":1630483008000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-S6-S3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,5,28]]},"references-count":37,"journal-issue":{"issue":"S6","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["2614"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-s6-s3","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,5,28]]},"assertion":[{"value":"28 May 2008","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S3"}}