{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T07:03:20Z","timestamp":1774422200417,"version":"3.50.1"},"reference-count":93,"publisher":"Springer Science and Business Media LLC","issue":"S17","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/1471-2105-15-s17-s4","type":"journal-article","created":{"date-parts":[[2015,6,18]],"date-time":"2015-06-18T18:00:23Z","timestamp":1434650423000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":72,"title":["Improving protein order-disorder classification using charge-hydropathy plots"],"prefix":"10.1186","volume":"15","author":[{"given":"Fei","family":"Huang","sequence":"first","affiliation":[]},{"given":"Christopher J","family":"Oldfield","sequence":"additional","affiliation":[]},{"given":"Bin","family":"Xue","sequence":"additional","affiliation":[]},{"given":"Wei-Lun","family":"Hsu","sequence":"additional","affiliation":[]},{"given":"Jingwei","family":"Meng","sequence":"additional","affiliation":[]},{"given":"Xiaowen","family":"Liu","sequence":"additional","affiliation":[]},{"given":"Li","family":"Shen","sequence":"additional","affiliation":[]},{"given":"Pedro","family":"Romero","sequence":"additional","affiliation":[]},{"given":"Vladimir N","family":"Uversky","sequence":"additional","affiliation":[]},{"given":"A Keith","family":"Dunker","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2014,12,16]]},"reference":[{"key":"6761_CR1","first-page":"473","volume-title":"Pac Symp Biocomput Pac Symp Biocomput","author":"AK Dunker","year":"1998","unstructured":"Dunker AK, Garner E, Guilliot S, Romero P, Albrecht K, Hart J, Obradovic Z, Kissinger C, Villafranca JE: Protein Disorder and the Evolution of Molecular Recognition: Theory, Predictions and Observations. Pac Symp Biocomput Pac Symp Biocomput. 1998, 473-484."},{"key":"6761_CR2","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1006\/jmbi.1999.3110","volume":"293","author":"PE Wright","year":"1999","unstructured":"Wright PE, Dyson HJ: Intrinsically Unstructured Proteins: Re-Assessing the Protein Structure-Function Paradigm. J Mol Biol. 1999, 293: 321-331. 10.1006\/jmbi.1999.3110.","journal-title":"J Mol Biol"},{"key":"6761_CR3","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1002\/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7","volume":"41","author":"VN Uversky","year":"2000","unstructured":"Uversky VN, Gillespie JR, Fink AL: Why Are \"natively Unfolded\" Proteins Unstructured under Physiologic Conditions?. Proteins Struct Funct Bioinforma. 2000, 41: 415-427. 10.1002\/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7.","journal-title":"Proteins Struct Funct Bioinforma"},{"key":"6761_CR4","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1016\/S1093-3263(00)00138-8","volume":"19","author":"AK Dunker","year":"2001","unstructured":"Dunker AK, Lawson JD, Brown CJ, Williams RM, Romero P, Oh JS, Oldfield CJ, Campen AM, Ratliff CM, Hipps KW, Ausio J, Nissen MS, Reeves R, Kang C, Kissinger CR, Bailey RW, Griswold MD, Chiu W, Garner EC, Obradovic Z: Intrinsically Disordered Protein. J Mol Graph Model. 2001, 19: 26-59. 10.1016\/S1093-3263(00)00138-8.","journal-title":"J Mol Graph Model"},{"key":"6761_CR5","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1016\/S0959-440X(02)00289-0","volume":"12","author":"HJ Dyson","year":"2002","unstructured":"Dyson HJ, Wright PE: Coupling of Folding and Binding for Unstructured Proteins. Curr Opin Struct Biol. 2002, 12: 54-60. 10.1016\/S0959-440X(02)00289-0.","journal-title":"Curr Opin Struct Biol"},{"key":"6761_CR6","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1016\/S0022-2836(02)00969-5","volume":"323","author":"LM Iakoucheva","year":"2002","unstructured":"Iakoucheva LM, Brown CJ, Lawson JD, Obradovi\u0107 Z, Dunker AK: Intrinsic Disorder in Cell-Signaling and Cancer-Associated Proteins. J Mol Biol. 2002, 323: 573-584. 10.1016\/S0022-2836(02)00969-5.","journal-title":"J Mol Biol"},{"key":"6761_CR7","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1016\/j.jmb.2004.02.002","volume":"337","author":"JJ Ward","year":"2004","unstructured":"Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT: Prediction and Functional Analysis of Native Disorder in Proteins from the Three Kingdoms of Life. J Mol Biol. 2004, 337: 635-645. 10.1016\/j.jmb.2004.02.002.","journal-title":"J Mol Biol"},{"key":"6761_CR8","first-page":"128","volume-title":"Pac Symp Biocomput Pac Symp Biocomput","author":"F Huang","year":"2012","unstructured":"Huang F, Oldfield C, Meng J, Hsu W-L, Xue B, Uversky VN, Romero P, Dunker AK: Subclassifying Disordered Proteins by the CH-CDF Plot Method. Pac Symp Biocomput Pac Symp Biocomput. 2012, 128-139."},{"key":"6761_CR9","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1038\/nrm1589","volume":"6","author":"HJ Dyson","year":"2005","unstructured":"Dyson HJ, Wright PE: Intrinsically Unstructured Proteins and Their Functions. Nat Rev Mol Cell Biol. 2005, 6: 197-208. 10.1038\/nrm1589.","journal-title":"Nat Rev Mol Cell Biol"},{"key":"6761_CR10","doi-asserted-by":"publisher","first-page":"6573","DOI":"10.1021\/bi012159+","volume":"41","author":"AK Dunker","year":"2002","unstructured":"Dunker AK, Brown CJ, Lawson JD, Iakoucheva LM, Obradovi\u0107 Z: Intrinsic Disorder and Protein Function. Biochemistry (Mosc). 2002, 41: 6573-6582. 10.1021\/bi012159+.","journal-title":"Biochemistry (Mosc)"},{"key":"6761_CR11","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/S0065-3233(02)62004-2","volume":"62","author":"AK Dunker","year":"2002","unstructured":"Dunker AK, Brown CJ, Obradovic Z: Identification and Functions of Usefully Disordered Proteins. Adv Protein Chem. 2002, 62: 25-49.","journal-title":"Adv Protein Chem"},{"key":"6761_CR12","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1007\/s11103-011-9803-z","volume":"77","author":"X Sun","year":"2011","unstructured":"Sun X, Xue B, Jones WT, Rikkerink E, Dunker AK, Uversky VN: A Functionally Required Unfoldome from the Plant Kingdom: Intrinsically Disordered N-Terminal Domains of GRAS Proteins Are Involved in Molecular Recognition during Plant Development. Plant Mol Biol. 2011, 77: 205-223. 10.1007\/s11103-011-9803-z.","journal-title":"Plant Mol Biol"},{"key":"6761_CR13","doi-asserted-by":"publisher","first-page":"1882","DOI":"10.1021\/pr060392u","volume":"6","author":"H Xie","year":"2007","unstructured":"Xie H, Vucetic S, Iakoucheva LM, Oldfield CJ, Dunker AK, Uversky VN, Obradovic Z: Functional Anthology of Intrinsic Disorder. 1. Biological Processes and Functions of Proteins with Long Disordered Regions. J Proteome Res. 2007, 6: 1882-1898. 10.1021\/pr060392u.","journal-title":"J Proteome Res"},{"key":"6761_CR14","doi-asserted-by":"publisher","first-page":"1899","DOI":"10.1021\/pr060393m","volume":"6","author":"S Vucetic","year":"2007","unstructured":"Vucetic S, Xie H, Iakoucheva LM, Oldfield CJ, Dunker AK, Obradovic Z, Uversky VN: Functional Anthology of Intrinsic Disorder. 2. Cellular Components, Domains, Technical Terms, Developmental Processes, and Coding Sequence Diversities Correlated with Long Disordered Regions. J Proteome Res. 2007, 6: 1899-1916. 10.1021\/pr060393m.","journal-title":"J Proteome Res"},{"key":"6761_CR15","doi-asserted-by":"publisher","first-page":"1917","DOI":"10.1021\/pr060394e","volume":"6","author":"H Xie","year":"2007","unstructured":"Xie H, Vucetic S, Iakoucheva LM, Oldfield CJ, Dunker AK, Obradovic Z, Uversky VN: Functional Anthology of Intrinsic Disorder. 3. Ligands, Post-Translational Modifications, and Diseases Associated with Intrinsically Disordered Proteins. J Proteome Res. 2007, 6: 1917-1932. 10.1021\/pr060394e.","journal-title":"J Proteome Res"},{"key":"6761_CR16","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1002\/1097-0134(20010101)42:1<38::AID-PROT50>3.0.CO;2-3","volume":"42","author":"P Romero","year":"2001","unstructured":"Romero P, Obradovic Z, Li X, Garner EC, Brown CJ, Dunker AK: Sequence Complexity of Disordered Protein. Proteins Struct Funct Bioinforma. 2001, 42: 38-48. 10.1002\/1097-0134(20010101)42:1<38::AID-PROT50>3.0.CO;2-3.","journal-title":"Proteins Struct Funct Bioinforma"},{"key":"6761_CR17","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1186\/1471-2105-7-208","volume":"7","author":"K Peng","year":"2006","unstructured":"Peng K, Radivojac P, Vucetic S, Dunker AK, Obradovic Z: Length-Dependent Prediction of Protein Intrinsic Disorder. BMC Bioinformatics. 2006, 7: 208-10.1186\/1471-2105-7-208.","journal-title":"BMC Bioinformatics"},{"key":"6761_CR18","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1142\/S0219720005000886","volume":"3","author":"K Peng","year":"2005","unstructured":"Peng K, Vucetic S, Radivojac P, Brown CJ, Dunker AK, Obradovic Z: Optimizing Long Intrinsic Disorder Predictors with Protein Evolutionary Information. J Bioinform Comput Biol. 2005, 3: 35-60. 10.1142\/S0219720005000886.","journal-title":"J Bioinform Comput Biol"},{"key":"6761_CR19","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1016\/j.bbapap.2010.01.011","volume":"1804","author":"B Xue","year":"2010","unstructured":"Xue B, Dunbrack RL, Williams RW, Dunker AK, Uversky VN: PONDR-FIT: A Meta-Predictor of Intrinsically Disordered Amino Acids. Biochim Biophys Acta BBA - Proteins Proteomics. 2010, 1804: 996-1010. 10.1016\/j.bbapap.2010.01.011.","journal-title":"Biochim Biophys Acta BBA - Proteins Proteomics"},{"key":"6761_CR20","doi-asserted-by":"publisher","first-page":"827","DOI":"10.1016\/j.jmb.2005.01.071","volume":"347","author":"Z Doszt\u00e1nyi","year":"2005","unstructured":"Doszt\u00e1nyi Z, Csizm\u00f3k V, Tompa P, Simon I: The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins. J Mol Biol. 2005, 347: 827-839. 10.1016\/j.jmb.2005.01.071.","journal-title":"J Mol Biol"},{"key":"6761_CR21","doi-asserted-by":"publisher","first-page":"3433","DOI":"10.1093\/bioinformatics\/bti541","volume":"21","author":"Z Doszt\u00e1nyi","year":"2005","unstructured":"Doszt\u00e1nyi Z, Csizmok V, Tompa P, Simon I: IUPred: Web Server for the Prediction of Intrinsically Unstructured Regions of Proteins Based on Estimated Energy Content. Bioinformatics. 2005, 21: 3433-3434. 10.1093\/bioinformatics\/bti541.","journal-title":"Bioinformatics"},{"key":"6761_CR22","doi-asserted-by":"publisher","first-page":"2138","DOI":"10.1093\/bioinformatics\/bth195","volume":"20","author":"JJ Ward","year":"2004","unstructured":"Ward JJ, McGuffin LJ, Bryson K, Buxton BF, Jones DT: The DISOPRED Server for the Prediction of Protein Disorder. Bioinformatics. 2004, 20: 2138-2139. 10.1093\/bioinformatics\/bth195.","journal-title":"Bioinformatics"},{"key":"6761_CR23","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1080\/073911012010525022","volume":"29","author":"T Zhang","year":"2012","unstructured":"Zhang T, Faraggi E, Xue B, Dunker AK, Uversky VN, Zhou Y: SPINE-D: Accurate Prediction of Short and Long Disordered Regions by a Single Neural-Network Based Method. J Biomol Struct X00026 Dyn. 2012, 29: 799-813. 10.1080\/073911012010525022.","journal-title":"J Biomol Struct X00026 Dyn"},{"key":"6761_CR24","doi-asserted-by":"publisher","first-page":"3435","DOI":"10.1093\/bioinformatics\/bti537","volume":"21","author":"J Prilusky","year":"2005","unstructured":"Prilusky J, Felder CE, Zeev-Ben-Mordehai T, Rydberg EH, Man O, Beckmann JS, Silman I, Sussman JL: FoldIndex\u00a9: A Simple Tool to Predict Whether a given Protein Sequence Is Intrinsically Unfolded. Bioinformatics. 2005, 21: 3435-3438. 10.1093\/bioinformatics\/bti537.","journal-title":"Bioinformatics"},{"key":"6761_CR25","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1002\/prot.22586","volume":"77","author":"O Noivirt-Brik","year":"2009","unstructured":"Noivirt-Brik O, Prilusky J, Sussman JL: Assessment of Disorder Predictions in CASP8. Proteins Struct Funct Bioinforma. 2009, 77: 210-216. 10.1002\/prot.22586.","journal-title":"Proteins Struct Funct Bioinforma"},{"key":"6761_CR26","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1002\/prot.23161","volume":"79","author":"B Monastyrskyy","year":"2011","unstructured":"Monastyrskyy B, Fidelis K, Moult J, Tramontano A, Kryshtafovych A: Evaluation of Disorder Predictions in CASP9. Proteins Struct Funct Bioinforma. 2011, 79: 107-118. 10.1002\/prot.23161.","journal-title":"Proteins Struct Funct Bioinforma"},{"key":"6761_CR27","doi-asserted-by":"publisher","first-page":"929","DOI":"10.1038\/cr.2009.87","volume":"19","author":"B He","year":"2009","unstructured":"He B, Wang K, Liu Y, Xue B, Uversky VN, Dunker AK: Predicting Intrinsic Disorder in Proteins: An Overview. Cell Res. 2009, 19: 929-949. 10.1038\/cr.2009.87.","journal-title":"Cell Res"},{"key":"6761_CR28","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1039\/C1MB05207A","volume":"8","author":"X Deng","year":"2011","unstructured":"Deng X, Eickholt J, Cheng J: A Comprehensive Overview of Computational Protein Disorder Prediction Methods. Mol Biosyst. 2011, 8: 114-121.","journal-title":"Mol Biosyst"},{"key":"6761_CR29","doi-asserted-by":"publisher","first-page":"6","DOI":"10.2174\/138920312799277938","volume":"13","author":"Z-L Peng","year":"2012","unstructured":"Peng Z-L, Kurgan L: Comprehensive Comparative Assessment of in-Silico Predictors of Disordered Regions. Curr Protein Pept Sci. 2012, 13: 6-18. 10.2174\/138920312799277938.","journal-title":"Curr Protein Pept Sci"},{"key":"6761_CR30","doi-asserted-by":"publisher","first-page":"1123","DOI":"10.1042\/bst0061123","volume":"6","author":"RJ Williams","year":"1978","unstructured":"Williams RJ: The Conformational Mobility of Proteins and Its Functional Significance. Biochem Soc Trans. 1978, 6: 1123-1126.","journal-title":"Biochem Soc Trans"},{"key":"6761_CR31","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1016\/0022-2836(82)90515-0","volume":"157","author":"J Kyte","year":"1982","unstructured":"Kyte J, Doolittle RF: A Simple Method for Displaying the Hydropathic Character of a Protein. J Mol Biol. 1982, 157: 105-132. 10.1016\/0022-2836(82)90515-0.","journal-title":"J Mol Biol"},{"key":"6761_CR32","doi-asserted-by":"crossref","first-page":"2211","DOI":"10.1016\/S0021-9258(19)77210-X","volume":"246","author":"Y Nozaki","year":"1971","unstructured":"Nozaki Y, Tanford C: The Solubility of Amino Acids and Two Glycine Peptides in Aqueous Ethanol and Dioxane Solutions ESTABLISHMENT OF A HYDROPHOBICITY SCALE. J Biol Chem. 1971, 246: 2211-2217.","journal-title":"J Biol Chem"},{"key":"6761_CR33","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1016\/S0006-3495(85)83877-7","volume":"47","author":"HR Guy","year":"1985","unstructured":"Guy HR: Amino Acid Side-Chain Partition Energies and Distribution of Residues in Soluble Proteins. Biophys J. 1985, 47: 61-70. 10.1016\/S0006-3495(85)83877-7.","journal-title":"Biophys J"},{"key":"6761_CR34","doi-asserted-by":"publisher","first-page":"534","DOI":"10.1021\/ma00145a039","volume":"18","author":"S Miyazawa","year":"1985","unstructured":"Miyazawa S, Jernigan RL: Estimation of Effective Interresidue Contact Energies from Protein Crystal Structures: Quasi-Chemical Approximation. Macromolecules. 1985, 18: 534-552. 10.1021\/ma00145a039.","journal-title":"Macromolecules"},{"key":"6761_CR35","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1038\/275673a0","volume":"275","author":"P Manavalan","year":"1978","unstructured":"Manavalan P, Ponnuswamy PK: Hydrophobic Character of Amino Acid Residues in Globular Proteins. Nature. 1978, 275: 673-674. 10.1038\/275673a0.","journal-title":"Nature"},{"key":"6761_CR36","first-page":"369","volume":"18","author":"J-L Fauchere","year":"1983","unstructured":"Fauchere J-L, Pliska VE: Hydrophobic Parameters Pi of Amino Acid Side Chains from Partitioning of N-Acetyl-Amino-Acid Amides. Eur J Med Chem. 1983, 18: 369-357.","journal-title":"Eur J Med Chem"},{"key":"6761_CR37","doi-asserted-by":"publisher","first-page":"834","DOI":"10.1126\/science.4023714","volume":"229","author":"GD Rose","year":"1985","unstructured":"Rose GD, Geselowitz AR, Lesser GJ, Lee RH, Zehfus MH: Hydrophobicity of Amino Acid Residues in Globular Proteins. Science. 1985, 229: 834-838. 10.1126\/science.4023714.","journal-title":"Science"},{"key":"6761_CR38","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1016\/0022-2836(83)90041-4","volume":"171","author":"RM Sweet","year":"1983","unstructured":"Sweet RM, Eisenberg D: Correlation of Sequence Hydrophobicities Measures Similarity in Three-Dimensional Protein Structure. J Mol Biol. 1983, 171: 479-488. 10.1016\/0022-2836(83)90041-4.","journal-title":"J Mol Biol"},{"key":"6761_CR39","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1016\/0003-2697(91)90045-U","volume":"193","author":"SD Black","year":"1991","unstructured":"Black SD, Mould DR: Development of Hydrophobicity Parameters to Analyze Proteins Which Bear Post- or Cotranslational Modifications. Anal Biochem. 1991, 193: 72-82. 10.1016\/0003-2697(91)90045-U.","journal-title":"Anal Biochem"},{"key":"6761_CR40","doi-asserted-by":"publisher","first-page":"3824","DOI":"10.1073\/pnas.78.6.3824","volume":"78","author":"TP Hopp","year":"1981","unstructured":"Hopp TP, Woods KR: Prediction of Protein Antigenic Determinants from Amino Acid Sequences. Proc Natl Acad Sci USA. 1981, 78: 3824-3828. 10.1073\/pnas.78.6.3824.","journal-title":"Proc Natl Acad Sci USA"},{"key":"6761_CR41","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1016\/0003-9861(74)90352-X","volume":"161","author":"HB Bull","year":"1974","unstructured":"Bull HB, Breese K: Surface Tension of Amino Acid Solutions: A Hydrophobicity Scale of the Amino Acid Residues. Arch Biochem Biophys. 1974, 161: 665-670. 10.1016\/0003-9861(74)90352-X.","journal-title":"Arch Biochem Biophys"},{"key":"6761_CR42","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1002\/prot.340020207","volume":"2","author":"DJ Abraham","year":"1987","unstructured":"Abraham DJ, Leo AJ: Extension of the Fragment Method to Calculate Amino Acid Zwitterion and Side Chain Partition Coefficients. Proteins Struct Funct Bioinforma. 1987, 2: 130-152. 10.1002\/prot.340020207.","journal-title":"Proteins Struct Funct Bioinforma"},{"key":"6761_CR43","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/0022-2836(76)90191-1","volume":"105","author":"C Chothia","year":"1976","unstructured":"Chothia C: The Nature of the Accessible and Buried Surfaces in Proteins. J Mol Biol. 1976, 105: 1-12. 10.1016\/0022-2836(76)90191-1.","journal-title":"J Mol Biol"},{"key":"6761_CR44","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1016\/0022-2836(88)90540-2","volume":"200","author":"MA Roseman","year":"1988","unstructured":"Roseman MA: Hydrophilicity of Polar Amino Acid Side-Chains Is Markedly Reduced by Flanking Peptide Bonds. J Mol Biol. 1988, 200: 513-522. 10.1016\/0022-2836(88)90540-2.","journal-title":"J Mol Biol"},{"key":"6761_CR45","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1016\/0167-4838(86)90295-5","volume":"869","author":"PA J K Mohana Rao","year":"1986","unstructured":"J K Mohana Rao PA: A Conformational Preference Parameter to Predict Helices in Integral Membrane Proteins. Biochim Biophys Acta. 1986, 869: 197-214. 10.1016\/0167-4838(86)90295-5.","journal-title":"Biochim Biophys Acta"},{"key":"6761_CR46","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1038\/277491a0","volume":"277","author":"J Janin","year":"1979","unstructured":"Janin J: Surface and inside Volumes in Globular Proteins. Nature. 1979, 277: 491-492. 10.1038\/277491a0.","journal-title":"Nature"},{"key":"6761_CR47","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1016\/0022-2836(84)90309-7","volume":"179","author":"D Eisenberg","year":"1984","unstructured":"Eisenberg D, Schwarz E, Komaromy M, Wall R: Analysis of Membrane and Surface Protein Sequences with the Hydrophobic Moment Plot. J Mol Biol. 1984, 179: 125-142. 10.1016\/0022-2836(84)90309-7.","journal-title":"J Mol Biol"},{"key":"6761_CR48","doi-asserted-by":"publisher","first-page":"4240","DOI":"10.1021\/ja00881a009","volume":"84","author":"C Tanford","year":"1962","unstructured":"Tanford C: Contribution of Hydrophobic Interactions to the Stability of the Globular Conformation of Proteins. J Am Chem Soc. 1962, 84: 4240-4247. 10.1021\/ja00881a009.","journal-title":"J Am Chem Soc"},{"key":"6761_CR49","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1016\/0014-5793(85)80374-4","volume":"188","author":"GW Welling","year":"1985","unstructured":"Welling GW, Weijer WJ, van der Zee R, Welling-Wester S: Prediction of Sequential Antigenic Regions in Proteins. FEBS Lett. 1985, 188: 215-218. 10.1016\/0014-5793(85)80374-4.","journal-title":"FEBS Lett"},{"key":"6761_CR50","doi-asserted-by":"publisher","first-page":"849","DOI":"10.1021\/bi00507a030","volume":"20","author":"R Wolfenden","year":"1981","unstructured":"Wolfenden R, Andersson L, Cullis PM, Southgate CCB: Affinities of Amino Acid Side Chains for Solvent Water. Biochemistry (Mosc). 1981, 20: 849-855. 10.1021\/bi00507a030.","journal-title":"Biochemistry (Mosc)"},{"key":"6761_CR51","doi-asserted-by":"publisher","first-page":"368","DOI":"10.1093\/nar\/27.1.368","volume":"27","author":"S Kawashima","year":"1999","unstructured":"Kawashima S, Ogata H, Kanehisa M: AAindex: Amino Acid Index Database. Nucleic Acids Res. 1999, 27: 368-369. 10.1093\/nar\/27.1.368.","journal-title":"Nucleic Acids Res"},{"key":"6761_CR52","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1093\/nar\/28.1.374","volume":"28","author":"S Kawashima","year":"2000","unstructured":"Kawashima S, Kanehisa M: AAindex: Amino Acid Index Database. Nucleic Acids Res. 2000, 28: 374-10.1093\/nar\/28.1.374.","journal-title":"Nucleic Acids Res"},{"key":"6761_CR53","doi-asserted-by":"publisher","first-page":"D202","DOI":"10.1093\/nar\/gkm998","volume":"36","author":"S Kawashima","year":"2008","unstructured":"Kawashima S, Pokarowski P, Pokarowska M, Kolinski A, Katayama T, Kanehisa M: AAindex: Amino Acid Index Database, Progress Report 2008. Nucleic Acids Res. 2008, 36: D202-205. 10.1093\/nar\/gkn255.","journal-title":"Nucleic Acids Res"},{"key":"6761_CR54","doi-asserted-by":"publisher","first-page":"W597","DOI":"10.1093\/nar\/gks400","volume":"40","author":"P Artimo","year":"2012","unstructured":"Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E, Grosdidier A, Hernandez C, Ioannidis V, Kuznetsov D, Liechti R, Moretti S, Mostaguir K, Redaschi N, Rossier G, Xenarios I, Stockinger H: ExPASy: SIB Bioinformatics Resource Portal. Nucleic Acids Res. 2012, 40: W597-W603. 10.1093\/nar\/gks400.","journal-title":"Nucleic Acids Res"},{"key":"6761_CR55","first-page":"531","volume":"112","author":"MR Wilkins","year":"1999","unstructured":"Wilkins MR, Gasteiger E, Bairoch A, Sanchez JC, Williams KL, Appel RD, Hochstrasser DF: Protein Identification and Analysis Tools in the ExPASy Server. Methods Mol Biol Clifton NJ. 1999, 112: 531-552.","journal-title":"Methods Mol Biol Clifton NJ"},{"key":"6761_CR56","doi-asserted-by":"publisher","first-page":"956","DOI":"10.2174\/092986608785849164","volume":"15","author":"A Campen","year":"2008","unstructured":"Campen A, Williams RM, Brown CJ, Meng J, Uversky VN, Dunker AK: TOP-IDP-Scale: A New Amino Acid Scale Measuring Propensity for Intrinsic Disorder. Protein Pept Lett. 2008, 15: 956-963. 10.2174\/092986608785849164.","journal-title":"Protein Pept Lett"},{"key":"6761_CR57","doi-asserted-by":"publisher","first-page":"2871","DOI":"10.1110\/ps.04881304","volume":"13","author":"SO Garbuzynskiy","year":"2004","unstructured":"Garbuzynskiy SO, Lobanov MY, Galzitskaya OV: To Be Folded or to Be Unfolded?. Protein Sci Publ Protein Soc. 2004, 13: 2871-2877.","journal-title":"Protein Sci Publ Protein Soc"},{"key":"6761_CR58","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1002\/prot.340190207","volume":"19","author":"M Vihinen","year":"1994","unstructured":"Vihinen M, Torkkila E, Riikonen P: Accuracy of Protein Flexibility Predictions. Proteins. 1994, 19: 141-149. 10.1002\/prot.340190207.","journal-title":"Proteins"},{"key":"6761_CR59","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1093\/bioinformatics\/bth476","volume":"21","author":"S Vucetic","year":"2005","unstructured":"Vucetic S, Obradovic Z, Vacic V, Radivojac P, Peng K, Iakoucheva LM, Cortese MS, Lawson JD, Brown CJ, Sikes JG, Newton CD, Dunker AK: DisProt: A Database of Protein Disorder. Bioinforma Oxf Engl. 2005, 21: 137-140. 10.1093\/bioinformatics\/bth476.","journal-title":"Bioinforma Oxf Engl"},{"key":"6761_CR60","doi-asserted-by":"publisher","first-page":"D786","DOI":"10.1093\/nar\/gkl893","volume":"35","author":"M Sickmeier","year":"2007","unstructured":"Sickmeier M, Hamilton JA, LeGall T, Vacic V, Cortese MS, Tantos A, Szabo B, Tompa P, Chen J, Uversky VN, Obradovic Z, Dunker AK: DisProt: The Database of Disordered Proteins. Nucleic Acids Res. 2007, 35: D786-D793. 10.1093\/nar\/gkl893.","journal-title":"Nucleic Acids Res"},{"key":"6761_CR61","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1186\/1471-2105-8-211","volume":"8","author":"V Vacic","year":"2007","unstructured":"Vacic V, Uversky VN, Dunker AK, Lonardi S: Composition Profiler: A Tool for Discovery and Visualization of Amino Acid Composition Differences. BMC Bioinformatics. 2007, 8: 211-10.1186\/1471-2105-8-211.","journal-title":"BMC Bioinformatics"},{"key":"6761_CR62","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1145\/1961189.1961199","volume":"2","author":"C-C Chang","year":"2011","unstructured":"Chang C-C, Lin C-J: LIBSVM: A Library for Support Vector Machines. ACM Trans Intell Syst Technol. 2011, 2: 1-27.","journal-title":"ACM Trans Intell Syst Technol"},{"key":"6761_CR63","first-page":"273","volume":"20","author":"C Cortes","year":"1995","unstructured":"Cortes C, Vapnik V: Support-Vector Networks. Mach Learn. 1995, 20: 273-297.","journal-title":"Mach Learn"},{"key":"6761_CR64","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1093\/protein\/2.2.93","volume":"2","author":"K Nakai","year":"1988","unstructured":"Nakai K, Kidera A, Kanehisa M: Cluster Analysis of Amino Acid Indices for Prediction of Protein Structure and Function. Protein Eng. 1988, 2: 93-100. 10.1093\/protein\/2.2.93.","journal-title":"Protein Eng"},{"key":"6761_CR65","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/protein\/9.1.27","volume":"9","author":"K Tomii","year":"1996","unstructured":"Tomii K, Kanehisa M: Analysis of Amino Acid Indices and Mutation Matrices for Sequence Comparison and Structure Prediction of Proteins. Protein Eng. 1996, 9: 27-36. 10.1093\/protein\/9.1.27.","journal-title":"Protein Eng"},{"key":"6761_CR66","doi-asserted-by":"publisher","first-page":"2140","DOI":"10.1110\/ps.072980107","volume":"16","author":"NB Holladay","year":"2007","unstructured":"Holladay NB, Kinch LN, Grishin NV: Optimization of Linear Disorder Predictors Yields Tight Association between Crystallographic Disorder and Hydrophobicity. Protein Sci Publ Protein Soc. 2007, 16: 2140-2152. 10.1110\/ps.072980107.","journal-title":"Protein Sci Publ Protein Soc"},{"key":"6761_CR67","doi-asserted-by":"publisher","first-page":"1263","DOI":"10.1109\/TKDE.2008.239","volume":"21","author":"H He","year":"2009","unstructured":"He H, Garcia EA: Learning from Imbalanced Data. IEEE Trans Knowl Data Eng. 2009, 21: 1263-1284.","journal-title":"IEEE Trans Knowl Data Eng"},{"key":"6761_CR68","first-page":"1871","volume":"9","author":"R-E Fan","year":"2008","unstructured":"Fan R-E, Chang K-W, Hsieh C-J, Wang X-R, Lin C-J: LIBLINEAR: A Library for Large Linear Classification. J Mach Learn Res. 2008, 9: 1871-1874.","journal-title":"J Mach Learn Res"},{"key":"6761_CR69","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1110\/ps.03128904","volume":"13","author":"P Radivojac","year":"2004","unstructured":"Radivojac P, Obradovic Z, Smith DK, Zhu G, Vucetic S, Brown CJ, Lawson JD, Dunker AK: Protein Flexibility and Intrinsic Disorder. Protein Sci Publ Protein Soc. 2004, 13: 71-80. 10.1110\/ps.03128904.","journal-title":"Protein Sci Publ Protein Soc"},{"key":"6761_CR70","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1007\/BF00175354","volume":"4","author":"D Whitley","year":"1994","unstructured":"Whitley D: A Genetic Algorithm Tutorial. Stat Comput. 1994, 4: 65-85.","journal-title":"Stat Comput"},{"key":"6761_CR71","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1007\/978-3-642-24446-9_4","volume-title":"Multimodal Brain Image Anal","author":"L Shen","year":"2011","unstructured":"Shen L, Kim S, Qi Y, Inlow M, Swaminathan S, Nho K, Wan J, Risacher SL, Shaw LM, Trojanowski JQ, Weiner MW, Saykin AJ: Identifying Neuroimaging and Proteomic Biomarkers for MCI and AD via the Elastic Net. Multimodal Brain Image Anal. Edited by: Liu T, Shen D, Ibanez L, Tao X. 2011, Springer Berlin Heidelberg, 27-34."},{"key":"6761_CR72","volume-title":"Pure Appl Chem","author":"JP Amend","year":"1997","unstructured":"Amend JP, Helgeson HC: Solubilities of the Common L-A-Amino Acids as a Function of Temperature and Solution pH. Pure Appl Chem. 1997, 69:"},{"key":"6761_CR73","doi-asserted-by":"publisher","first-page":"5552","DOI":"10.1021\/ja01650a082","volume":"76","author":"A Berger","year":"1954","unstructured":"Berger A, Kurtz J, Katchalski E: Poly-L-Proline. J Am Chem Soc. 1954, 76: 5552-5554. 10.1021\/ja01650a082.","journal-title":"J Am Chem Soc"},{"key":"6761_CR74","doi-asserted-by":"publisher","first-page":"5","DOI":"10.4161\/idp.24360","volume":"1","author":"F-X Theillet","year":"2013","unstructured":"Theillet F-X, Kalmar L, Tompa P, Han K-H, Selenko P, Dunker AK, Daughdrill GW, Uversky VN: The Alphabet of Intrinsic Disorder: I. Act like a Pro: On the Abundance and Roles of Proline Residues in. Intrinsically Disord Proteins. 2013, 1: 5-17.","journal-title":"Intrinsically Disord Proteins"},{"key":"6761_CR75","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1016\/j.jmb.2006.07.087","volume":"362","author":"A Mohan","year":"2006","unstructured":"Mohan A, Oldfield CJ, Radivojac P, Vacic V, Cortese MS, Dunker AK, Uversky VN: Analysis of Molecular Recognition Features (MoRFs). J Mol Biol. 2006, 362: 1043-1059. 10.1016\/j.jmb.2006.07.087.","journal-title":"J Mol Biol"},{"key":"6761_CR76","doi-asserted-by":"publisher","first-page":"2351","DOI":"10.1021\/pr0701411","volume":"6","author":"V Vacic","year":"2007","unstructured":"Vacic V, Oldfield CJ, Mohan A, Radivojac P, Cortese MS, Uversky VN, Dunker AK: Characterization of Molecular Recognition Features, MoRFs, and Their Binding Partners. J Proteome Res. 2007, 6: 2351-2366. 10.1021\/pr0701411.","journal-title":"J Proteome Res"},{"key":"6761_CR77","doi-asserted-by":"publisher","first-page":"12454","DOI":"10.1021\/bi050736e","volume":"44","author":"CJ Oldfield","year":"2005","unstructured":"Oldfield CJ, Cheng Y, Cortese MS, Romero P, Uversky VN, Dunker AK: Coupled Folding and Binding with A-Helix-Forming Molecular Recognition Elements\u2020. Biochemistry (Mosc). 2005, 44: 12454-12470. 10.1021\/bi050736e.","journal-title":"Biochemistry (Mosc)"},{"key":"6761_CR78","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1002\/pro.2207","volume":"22","author":"W-L Hsu","year":"2013","unstructured":"Hsu W-L, Oldfield CJ, Xue B, Meng J, Huang F, Romero P, Uversky VN, Dunker AK: Exploring the Binding Diversity of Intrinsically Disordered Proteins Involved in One-to-Many Binding. Protein Sci. 2013, 22: 258-273. 10.1002\/pro.2207.","journal-title":"Protein Sci"},{"key":"6761_CR79","doi-asserted-by":"publisher","first-page":"1469","DOI":"10.1016\/j.febslet.2009.03.070","volume":"583","author":"B Xue","year":"2009","unstructured":"Xue B, Oldfield CJ, Dunker AK, Uversky VN: CDF It All: Consensus Prediction of Intrinsically Disordered Proteins Based on Various Cumulative Distribution Functions. FEBS Lett. 2009, 583: 1469-1474. 10.1016\/j.febslet.2009.03.070.","journal-title":"FEBS Lett"},{"key":"6761_CR80","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1016\/S0022-2836(77)80200-3","volume":"112","author":"FC Bernstein","year":"1977","unstructured":"Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M: The Protein Data Bank: A Computer-Based Archival File for Macromolecular Structures. J Mol Biol. 1977, 112: 535-542. 10.1016\/S0022-2836(77)80200-3.","journal-title":"J Mol Biol"},{"key":"6761_CR81","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: 403-410. 10.1016\/S0022-2836(05)80360-2.","journal-title":"J Mol Biol"},{"key":"6761_CR82","volume-title":"The Effect of Class Distribution on Classifier Learning: An Empirical Study","author":"G Weiss","year":"2001","unstructured":"Weiss G, Provost F: The Effect of Class Distribution on Classifier Learning: An Empirical Study. 2001"},{"key":"6761_CR83","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1007\/3-540-48229-6_9","volume-title":"Proc 8th Conf AI Med Eur Artif Intell Med","author":"J Laurikkala","year":"2001","unstructured":"Laurikkala J: Improving Identification of Difficult Small Classes by Balancing Class Distribution. Proc 8th Conf AI Med Eur Artif Intell Med. 2001, London, UK, UK: Springer-Verlag, 63-66."},{"key":"6761_CR84","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1111\/j.0824-7935.2004.t01-1-00228.x","volume":"20","author":"A Estabrooks","year":"2004","unstructured":"Estabrooks A, Jo T, Japkowicz N: A Multiple Resampling Method for Learning from Imbalanced Data Sets. Comput Intell. 2004, 20: 18-36. 10.1111\/j.0824-7935.2004.t01-1-00228.x.","journal-title":"Comput Intell"},{"key":"6761_CR85","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1613\/jair.953","volume":"16","author":"NV Chawla","year":"2002","unstructured":"Chawla NV, Bowyer KW, Hall LO, Kegelmeyer WP: SMOTE: Synthetic Minority Over-Sampling Technique. J Artif Intell Res. 2002, 16: 321-357.","journal-title":"J Artif Intell Res"},{"key":"6761_CR86","doi-asserted-by":"publisher","first-page":"878","DOI":"10.1007\/11538059_91","volume-title":"Adv Intell Comput","author":"H Han","year":"2005","unstructured":"Han H, Wang W-Y, Mao B-H: Borderline-SMOTE: A New Over-Sampling Method in Imbalanced Data Sets Learning. Adv Intell Comput. Edited by: Huang D-S, Zhang X-P, Huang G-B. 2005, Springer Berlin Heidelberg, 878-887."},{"key":"6761_CR87","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1136\/bmj.309.6947.102","volume":"309","author":"DG Altman","year":"1994","unstructured":"Altman DG, Bland JM: Diagnostic Tests 2: Predictive Values. BMJ. 1994, 309: 102-","journal-title":"BMJ"},{"key":"6761_CR88","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1002\/jmri.22466","volume":"33","author":"TF Heston","year":"2011","unstructured":"Heston TF: Standardizing Predictive Values in Diagnostic Imaging Research. J Magn Reson Imaging JMRI. 2011, 33: 505-10.1002\/jmri.22466. author reply 506-507","journal-title":"J Magn Reson Imaging JMRI"},{"key":"6761_CR89","doi-asserted-by":"publisher","first-page":"1773","DOI":"10.1002\/sim.1119","volume":"21","author":"RK Gunnarsson","year":"2002","unstructured":"Gunnarsson RK, Lanke J: The Predictive Value of Microbiologic Diagnostic Tests If Asymptomatic Carriers Are Present. Stat Med. 2002, 21: 1773-1785. 10.1002\/sim.1119.","journal-title":"Stat Med"},{"key":"6761_CR90","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1145\/1147234.1147236","volume":"8","author":"RB Rao","year":"2006","unstructured":"Rao RB, Krishnan S, Niculescu RS: Data Mining for Improved Cardiac Care. SIGKDD Explor Newsl. 2006, 8: 3-10.","journal-title":"SIGKDD Explor Newsl"},{"key":"6761_CR91","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1093\/bioinformatics\/16.5.412","volume":"16","author":"P Baldi","year":"2000","unstructured":"Baldi P, Brunak S, Chauvin Y, Andersen CAF, Nielsen H: Assessing the Accuracy of Prediction Algorithms for Classification: An Overview. Bioinformatics. 2000, 16: 412-424. 10.1093\/bioinformatics\/16.5.412.","journal-title":"Bioinformatics"},{"key":"6761_CR92","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1093\/clinchem\/39.4.561","volume":"39","author":"MH Zweig","year":"1993","unstructured":"Zweig MH, Campbell G: Receiver-Operating Characteristic (ROC) Plots: A Fundamental Evaluation Tool in Clinical Medicine. Clin Chem. 1993, 39: 561-577.","journal-title":"Clin Chem"},{"key":"6761_CR93","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1098\/rsta.1896.0007","volume":"187","author":"K Pearson","year":"1896","unstructured":"Pearson K: Mathematical Contributions to the Theory of Evolution. III. Regression, Heredity, and Panmixia. Philos Trans R Soc Lond Ser Contain Pap Math Phys Character. 1896, 187: 253-318. 10.1098\/rsta.1896.0007.","journal-title":"Philos Trans R Soc Lond Ser Contain Pap Math Phys Character"}],"updated-by":[{"DOI":"10.1186\/s12859-015-0646-5","type":"erratum","label":"Erratum","source":"publisher","updated":{"date-parts":[[2015,7,31]],"date-time":"2015-07-31T00:00:00Z","timestamp":1438300800000}}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-15-S17-S4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T18:49:04Z","timestamp":1630608544000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-15-S17-S4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,12]]},"references-count":93,"journal-issue":{"issue":"S17","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["6761"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-15-s17-s4","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,12]]},"assertion":[{"value":"16 December 2014","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S4"}}