{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T15:40:41Z","timestamp":1783611641457,"version":"3.55.0"},"reference-count":23,"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":[[2008,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>A protein structural class (PSC) belongs to the most basic but important classification in protein structures. The prediction technique of protein structural class has been developing for decades. Two popular indices are the amino-acid-frequency (AAF) based, and amino-acid-arrangement (AAA) with long-term correlation (LTC) \u2013 based indices. They were proposed in many works. Both indices have its pros and cons. For example, the AAF index focuses on a statistical analysis, while the AAA-LTC emphasizes the long-term, biological significance. Unfortunately, the datasets used in previous work were not very reliable for a small number of sequences with a high-sequence similarity.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>By modifying a statistical strategy, we proposed a new index method that combines probability and information theory together with a long-term correlation. We also proposed a numerically and biologically reliable dataset included more than 5700 sequences with a low sequence similarity. The results showed that the proposed approach has its high accuracy. Comparing with amino acid composition (AAC) index using a distance method, the accuracy of our approach has a 16\u201320% improvement for re-substitution test and about 6\u201311% improvement for cross-validation test. The values were about 23% and 15% for the component coupled method (CCM).<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>A new index method, combining probability and information theory together with a long-term correlation was proposed in this paper. The statistical method was improved significantly based on our new index. The cross validation test was conducted, and the result show the proposed method has a great improvement.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-9-s6-s5","type":"journal-article","created":{"date-parts":[[2008,5,28]],"date-time":"2008-05-28T18:15:46Z","timestamp":1211998546000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Protein structural class prediction based on an improved statistical strategy"],"prefix":"10.1186","volume":"9","author":[{"given":"Fei","family":"Gu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hang","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Ni","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2008,5,28]]},"reference":[{"key":"2616_CR1","doi-asserted-by":"publisher","first-page":"552","DOI":"10.1038\/261552a0","volume":"261","author":"M Levitt","year":"1976","unstructured":"Levitt M, Chothia C: Structural patterns in globular proteins. Nature. 1976, 261: 552-557. 10.1038\/261552a0.","journal-title":"Nature"},{"key":"2616_CR2","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1016\/j.bbrc.2005.06.128","volume":"334","author":"HB Shen","year":"2005","unstructured":"Shen HB, Yang J, Liu XJ, Chou KC: Using supervised fuzzy clustering to predict protein structural classes. Biochem Biophys Res Commun. 2005, 334: 577-581. 10.1016\/j.bbrc.2005.06.128.","journal-title":"Biochem Biophys Res Commun"},{"issue":"4","key":"2616_CR3","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1016\/j.bbrc.2004.07.059","volume":"321","author":"KC Chou","year":"2004","unstructured":"Chou KC, Cai YD: Predicting protein structural class byfunctional domain composition. Biochem Biophys Res Commun. 2004, 321 (4): 1007-1009. 10.1016\/j.bbrc.2004.07.059.","journal-title":"Biochem Biophys Res Commun"},{"issue":"1","key":"2616_CR4","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1016\/j.bbrc.2005.06.075","volume":"334","author":"KY Feng","year":"2005","unstructured":"Feng KY, Cai YD, Chou KC: Boosting classifier for predicting protein domain structural class. Biochem Biophys Res Commun. 2005, 334 (1): 213-217. 10.1016\/j.bbrc.2005.06.075.","journal-title":"Biochem Biophys Res Commun"},{"issue":"8","key":"2616_CR5","doi-asserted-by":"publisher","first-page":"729","DOI":"10.1023\/A:1020713915365","volume":"17","author":"GP Zhou","year":"1998","unstructured":"Zhou GP: An intriguing controversy over protein structural class prediction. J Protein Chem. 1998, 17 (8): 729-738. 10.1023\/A:1020713915365.","journal-title":"J Protein Chem"},{"issue":"5","key":"2616_CR6","doi-asserted-by":"publisher","first-page":"423","DOI":"10.2174\/138920305774329368","volume":"6","author":"KC Chou","year":"2005","unstructured":"Chou KC: Progress in protein structural class prediction and its impact to bioinformatics and proteomics. Curr Protein Pept Sci. 2005, 6 (5): 423-436. 10.2174\/138920305774329368.","journal-title":"Curr Protein Pept Sci"},{"issue":"8","key":"2616_CR7","doi-asserted-by":"publisher","first-page":"783","DOI":"10.1016\/S0300-9084(00)01161-5","volume":"82","author":"Y Cai","year":"2000","unstructured":"Cai Y, Zhou G: Prediction of protein structural classes by neural network. Biochimie. 2000, 82 (8): 783-785. 10.1016\/S0300-9084(00)01161-5.","journal-title":"Biochimie"},{"key":"2616_CR8","doi-asserted-by":"crossref","first-page":"1821","DOI":"10.1093\/oxfordjournals.jbchem.a133877","volume":"91","author":"K Nishkawa","year":"1982","unstructured":"Nishkawa K, Ooi T: Correlation of the amino acid composition of a protein to its structural and biological characters. J Biochem. 1982, 91: 1821-1824.","journal-title":"J Biochem"},{"key":"2616_CR9","doi-asserted-by":"publisher","first-page":"275","DOI":"10.3109\/10409239509083488","volume":"30","author":"KC Chou","year":"1995","unstructured":"Chou KC, Zhang CT: Prediction of protein structural classes. Crit Rev Biochem Mol Biol. 1995, 30: 275-349. 10.3109\/10409239509083488.","journal-title":"Crit Rev Biochem Mol Biol"},{"key":"2616_CR10","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1093\/protein\/11.7.523","volume":"11","author":"KC Chou","year":"1998","unstructured":"Chou KC, Maggiora GM: Domain structural class prediction. Protein Eng. 1998, 11: 523-538. 10.1093\/protein\/11.7.523.","journal-title":"Protein Eng"},{"key":"2616_CR11","volume-title":"Multivariate Analysis","author":"KV Mardia","year":"1979","unstructured":"Mardia KV, Kent JT, Bibby JM: Multivariate Analysis. 1979, Academic Press, London"},{"key":"2616_CR12","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1093\/oxfordjournals.jbchem.a135454","volume":"99","author":"H Nakashima","year":"1986","unstructured":"Nakashima H, Nishikawa K, Ooi T: The folding type of a protein is relevant to the amino acid composition. J Biochem. 1986, 99: 153-162.","journal-title":"J Biochem"},{"key":"2616_CR13","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1002\/prot.340210406","volume":"21","author":"KC Chou","year":"1995","unstructured":"Chou KC: A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins. 1995, 21: 319-344. 10.1002\/prot.340210406.","journal-title":"Proteins"},{"key":"2616_CR14","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1002\/(SICI)1097-0134(20000201)38:2<165::AID-PROT5>3.0.CO;2-V","volume":"38","author":"ZX Wang","year":"2000","unstructured":"Wang ZX, Yuan Z: How good is prediction of protein structural class by the component \u2013 coupled method. Proteins. 2000, 38: 165-175. 10.1002\/(SICI)1097-0134(20000201)38:2<165::AID-PROT5>3.0.CO;2-V.","journal-title":"Proteins"},{"issue":"1","key":"2616_CR15","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1002\/prot.1071","volume":"44","author":"GP Zhou","year":"2001","unstructured":"Zhou GP, Assa-Munt N: Some insights into protein structural class prediction. Proteins. 2001, 44 (1): 57-59. 10.1002\/prot.1071.","journal-title":"Proteins"},{"key":"2616_CR16","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1186\/1471-2105-2-3","volume":"2","author":"YD Cai","year":"2001","unstructured":"Cai YD, Liu XJ, Xu XB: Support vector machines for predicting protein structural class. BMC Bioinformatics. 2001, 2: 3-10.1186\/1471-2105-2-3.","journal-title":"BMC Bioinformatics"},{"key":"2616_CR17","doi-asserted-by":"publisher","first-page":"4219","DOI":"10.1046\/j.1432-1033.2002.03115.x","volume":"269","author":"RY Luo","year":"2002","unstructured":"Luo RY, Feng ZP, Liu JK: Prediction of protein structural class by amino acid and ploypeptide composition. Eur J Biochem. 2002, 269: 4219-4225. 10.1046\/j.1432-1033.2002.03115.x.","journal-title":"Eur J Biochem"},{"key":"2616_CR18","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1080\/07391102.2006.10507088","volume":"23","author":"QS Du","year":"2006","unstructured":"Du QS, Jiang ZQ, He WZ, Li DP, Chou KC: Amino acid principal component analysis (AAPCA) and its application in protein structural class prediction. J Biomol Struct Dyn. 2006, 23: 635-640.","journal-title":"J Biomol Struct Dyn"},{"key":"2616_CR19","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1046\/j.1432-1327.1999.00947.x","volume":"266","author":"WS Bu","year":"1999","unstructured":"Bu WS, Feng ZP, Zhang ZD, Zhang CT: Prediction of protein (domain) structural classes based on amino-acid index. Eur J Biochem. 1999, 266: 1043-1049. 10.1046\/j.1432-1327.1999.00947.x.","journal-title":"Eur J Biochem"},{"key":"2616_CR20","doi-asserted-by":"publisher","first-page":"1041","DOI":"10.1093\/protein\/12.12.1041","volume":"12","author":"WM Liu","year":"1999","unstructured":"Liu WM, Chou KC: Prediction of protein secondary structure content. Protein Eng. 1999, 12: 1041-1050. 10.1093\/protein\/12.12.1041.","journal-title":"Protein Eng"},{"key":"2616_CR21","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 protein database for the investigation of sequence and structures. J Mol Biol. 1995, 247: 536-540. 10.1006\/jmbi.1995.0159.","journal-title":"J Mol Biol"},{"key":"2616_CR22","doi-asserted-by":"publisher","first-page":"171","DOI":"10.2174\/1389203003381379","volume":"1","author":"KC Chou","year":"2000","unstructured":"Chou KC: Prediction of protein structural classes and subcellular locations. Curr Protein Pept Sci. 2000, 1: 171-208. 10.2174\/1389203003381379.","journal-title":"Curr Protein Pept Sci"},{"key":"2616_CR23","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"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-S6-S5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T07:56:46Z","timestamp":1630483006000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-S6-S5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,5]]},"references-count":23,"journal-issue":{"issue":"S6","published-print":{"date-parts":[[2008,5]]}},"alternative-id":["2616"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-s6-s5","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,5]]},"assertion":[{"value":"28 May 2008","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S5"}}