{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T17:11:30Z","timestamp":1773162690994,"version":"3.50.1"},"reference-count":32,"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":[[2016,12]]},"DOI":"10.1186\/s12859-016-1337-6","type":"journal-article","created":{"date-parts":[[2016,12,23]],"date-time":"2016-12-23T16:27:56Z","timestamp":1482510476000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":30,"title":["Prediction of HIV-1 protease cleavage site using a combination of sequence, structural, and physicochemical features"],"prefix":"10.1186","volume":"17","author":[{"given":"Onkar","family":"Singh","sequence":"first","affiliation":[]},{"given":"Emily Chia-Yu","family":"Su","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,12,23]]},"reference":[{"issue":"5112","key":"1337_CR1","doi-asserted-by":"crossref","first-page":"1273","DOI":"10.1126\/science.8493571","volume":"260","author":"RA Weiss","year":"1993","unstructured":"Weiss RA. How does HIV cause AIDS? Science. 1993;260(5112):1273\u20139.","journal-title":"Science"},{"issue":"1","key":"1337_CR2","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1039\/b208248a","volume":"1","author":"A Brik","year":"2003","unstructured":"Brik A, Wong CH. HIV-1 protease: mechanism and drug discovery. Org Biomol Chem. 2003;1(1):5\u201314.","journal-title":"Org Biomol Chem"},{"issue":"24","key":"1337_CR3","doi-asserted-by":"crossref","first-page":"2283","DOI":"10.1056\/NEJMp038194","volume":"349","author":"RC Gallo","year":"2003","unstructured":"Gallo RC, Montagnier L. The discovery of HIV as the cause of AIDS. N Engl J Med. 2003;349(24):2283\u20135.","journal-title":"N Engl J Med"},{"key":"1337_CR4","doi-asserted-by":"crossref","unstructured":"Verkhivker GM. Coarse-Grained Modeling of the HIV-1 Protease Binding Mechanisms: II. Folding Inhibition. In: Computational Intelligence Methods for Bioinformatics and Biostatistics. Springer Berlin Heidelberg; 2009. p. 13-24.","DOI":"10.1007\/978-3-642-02504-4_2"},{"issue":"1","key":"1337_CR5","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1002\/prot.21415","volume":"68","author":"A Kontijevskis","year":"2007","unstructured":"Kontijevskis A, Wikberg JE, Komorowski J. Computational proteomics analysis of HIV-1 protease interactome. Proteins. 2007;68(1):305\u201312.","journal-title":"Proteins"},{"key":"1337_CR6","first-page":"95","volume":"7","author":"Z Lv","year":"2015","unstructured":"Lv Z, Chu Y, Wang Y. HIV protease inhibitors: a review of molecular selectivity and toxicity. HIV AIDS (Auckl). 2015;7:95\u2013104.","journal-title":"HIV AIDS (Auckl)"},{"issue":"1","key":"1337_CR7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1006\/abio.1996.0001","volume":"233","author":"KC Chou","year":"1996","unstructured":"Chou KC. Prediction of human immunodeficiency virus protease cleavage sites in proteins. Anal Biochem. 1996;233(1):1\u201314.","journal-title":"Anal Biochem"},{"issue":"19","key":"1337_CR8","doi-asserted-by":"crossref","first-page":"12477","DOI":"10.1128\/JVI.79.19.12477-12486.2005","volume":"79","author":"L You","year":"2005","unstructured":"You L, Garwicz D, Rognvaldsson T. Comprehensive bioinformatic analysis of the specificity of human immunodeficiency virus type 1 protease. J Virol. 2005;79(19):12477\u201386.","journal-title":"J Virol"},{"issue":"1","key":"1337_CR9","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1016\/j.compbiolchem.2007.09.006","volume":"32","author":"H Kim","year":"2008","unstructured":"Kim H, Zhang Y, Heo Y-S, Oh H-B, Chen S-S. Specificity rule discovery in HIV-1 protease cleavage site analysis. Comput Biol Chem. 2008;32(1):72\u20139.","journal-title":"Comput Biol Chem"},{"issue":"3","key":"1337_CR10","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1016\/j.biosystems.2009.03.001","volume":"96","author":"H Ogul","year":"2009","unstructured":"Ogul H. Variable context Markov chains for HIV protease cleavage site prediction. Bio Systems. 2009;96(3):246\u201350.","journal-title":"Bio Systems"},{"issue":"3","key":"1337_CR11","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1007\/s00726-008-0076-z","volume":"36","author":"L Nanni","year":"2009","unstructured":"Nanni L, Lumini A. Using ensemble of classifiers for predicting HIV protease cleavage sites in proteins. Amino Acids. 2009;36(3):409\u201316.","journal-title":"Amino Acids"},{"issue":"2","key":"1337_CR12","doi-asserted-by":"crossref","first-page":"269","DOI":"10.6339\/JDS.2010.08(2).607","volume":"8","author":"S Jaeger","year":"2010","unstructured":"Jaeger S, Chen S-S. Information fusion for biological prediction. J Data Sci. 2010;8(2):269\u201388.","journal-title":"J Data Sci"},{"issue":"1\u20132","key":"1337_CR13","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1007\/s11010-009-0376-y","volume":"339","author":"X Li","year":"2010","unstructured":"Li X, Hu H, Shu L. Predicting human immunodeficiency virus protease cleavage sites in nonlinear projection space. Mol Cell Biochem. 2010;339(1\u20132):127\u201333.","journal-title":"Mol Cell Biochem"},{"issue":"24","key":"1337_CR14","doi-asserted-by":"crossref","first-page":"3415","DOI":"10.1093\/bioinformatics\/btr594","volume":"27","author":"NE Newell","year":"2011","unstructured":"Newell NE. Cascade detection for the extraction of localized sequence features; specificity results for HIV-1 protease and structure-function results for the Schellman loop. Bioinformatics. 2011;27(24):3415\u201322.","journal-title":"Bioinformatics"},{"issue":"7","key":"1337_CR15","first-page":"1757","volume":"22","author":"M G\u00f6k","year":"2012","unstructured":"G\u00f6k M, \u00d6zcerit AT. A new feature encoding scheme for HIV-1 protease cleavage site prediction. Neural Comput & Applic. 2012;22(7):1757\u201361.","journal-title":"Neural Comput & Applic"},{"issue":"11","key":"1337_CR16","doi-asserted-by":"crossref","first-page":"e50300","DOI":"10.1371\/journal.pone.0050300","volume":"7","author":"J Song","year":"2012","unstructured":"Song J, Tan H, Perry AJ, Akutsu T, Webb GI, Whisstock JC, Pike RN. PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites. PLoS One. 2012;7(11):e50300.","journal-title":"PLoS One"},{"issue":"3","key":"1337_CR17","first-page":"290","volume":"20","author":"B Niu","year":"2013","unstructured":"Niu B, Yuan XC, Roeper P, Su Q, Peng CR, Yin JY, Ding J, Li H, Lu WC. HIV-1 protease cleavage site prediction based on two-stage feature selection method. Protein Pept Lett. 2013;20(3):290\u20138.","journal-title":"Protein Pept Lett"},{"issue":"3","key":"1337_CR18","doi-asserted-by":"crossref","first-page":"e1002977","DOI":"10.1371\/journal.pcbi.1002977","volume":"9","author":"K Bozek","year":"2013","unstructured":"Bozek K, Lengauer T, Sierra S, Kaiser R, Domingues FS. Analysis of physicochemical and structural properties determining HIV-1 coreceptor usage. PLoS Comput Biol. 2013;9(3):e1002977.","journal-title":"PLoS Comput Biol"},{"issue":"8","key":"1337_CR19","doi-asserted-by":"crossref","first-page":"1204","DOI":"10.1093\/bioinformatics\/btu810","volume":"31","author":"T Rognvaldsson","year":"2015","unstructured":"Rognvaldsson T, You L, Garwicz D. State of the art prediction of HIV-1 protease cleavage sites. Bioinformatics. 2015;31(8):1204\u201310.","journal-title":"Bioinformatics"},{"key":"1337_CR20","doi-asserted-by":"crossref","unstructured":"Liu H, Shi X, Guo D, Zhao Z. Feature selection combined with neural network structure optimization for HIV-1 protease cleavage site prediction. BioMed Res Int. 2015;2015: Article ID 263586.","DOI":"10.1155\/2015\/263586"},{"key":"1337_CR21","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1186\/1472-6807-9-51","volume":"9","author":"B Petersen","year":"2009","unstructured":"Petersen B, Petersen TN, Andersen P, Nielsen M, Lundegaard C. A generic method for assignment of reliability scores applied to solvent accessibility predictions. BMC Struct Biol. 2009;9:51.","journal-title":"BMC Struct Biol"},{"issue":"1","key":"1337_CR22","doi-asserted-by":"crossref","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(1):374.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"1337_CR23","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1016\/j.jtbi.2010.12.024","volume":"273","author":"KC Chou","year":"2011","unstructured":"Chou KC. Some remarks on protein attribute prediction and pseudo amino acid composition. J Theor Biol. 2011;273(1):236\u201347.","journal-title":"J Theor Biol"},{"issue":"11","key":"1337_CR24","doi-asserted-by":"crossref","first-page":"5913","DOI":"10.1073\/pnas.95.11.5913","volume":"95","author":"M Levitt","year":"1998","unstructured":"Levitt M, Gerstein M. A unified statistical framework for sequence comparison and structure comparison. Proc Natl Acad Sci U S A. 1998;95(11):5913\u201320.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"1337_CR25","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1016\/S0920-5632(03)01524-X","volume":"119","author":"L Zhou","year":"2003","unstructured":"Zhou L, Lee F, Wilcox W, Christensen J. Magnetic polarizability of hadrons from lattice QCD. Nucl Phys B Proc Suppl. 2003;119:272\u20134.","journal-title":"Nucl Phys B Proc Suppl"},{"issue":"6837","key":"1337_CR26","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/35079225","volume":"411","author":"F Weinhold","year":"2001","unstructured":"Weinhold F. Chemistry: A new twist on molecular shape. Nature. 2001;411(6837):539\u201341.","journal-title":"Nature"},{"key":"1337_CR27","unstructured":"Nelson DL, Lehninger AL, Cox MM. Lehninger principles of biochemistry. Macmillan: Cambridge University Press, New York; 2008."},{"issue":"16","key":"1337_CR28","doi-asserted-by":"crossref","first-page":"4031","DOI":"10.1021\/ja984344p","volume":"121","author":"AE Counterman","year":"1999","unstructured":"Counterman AE, Clemmer DE. Volumes of individual amino acid residues in gas-phase peptide ions. J Am Chem Soc. 1999;121(16):4031\u20139.","journal-title":"J Am Chem Soc"},{"key":"1337_CR29","doi-asserted-by":"crossref","unstructured":"Wilson K, Walker J. Principles and techniques of biochemistry and molecular biology. Cambridge University Press; 2010.","DOI":"10.1017\/CBO9780511841477"},{"issue":"suppl 1","key":"1337_CR30","doi-asserted-by":"crossref","first-page":"S5","DOI":"10.1093\/bioinformatics\/18.suppl_1.S5","volume":"18","author":"A Narayanan","year":"2002","unstructured":"Narayanan A, Wu X, Yang ZR. Mining viral protease data to extract cleavage knowledge. Bioinformatics. 2002;18 suppl 1:S5\u201313.","journal-title":"Bioinformatics"},{"key":"1337_CR31","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1142\/9781860947575_0031","volume":"5","author":"L You","year":"2006","unstructured":"You L. Detection of cleavage sites for HIV-1 protease in native proteins. Comput Syst Bioinformatics Conf. 2006; 5:249\u201356.","journal-title":"Comput Syst Bioinformatics Conf."},{"issue":"3","key":"1337_CR32","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1016\/S0969-2126(02)00720-7","volume":"10","author":"M Prabu-Jeyabalan","year":"2002","unstructured":"Prabu-Jeyabalan M, Nalivaika E, Schiffer CA. Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes. Structure. 2002;10(3):369\u201381.","journal-title":"Structure"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1337-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,19]],"date-time":"2022-07-19T20:53:13Z","timestamp":1658263993000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-016-1337-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,12]]},"references-count":32,"journal-issue":{"issue":"S17","published-print":{"date-parts":[[2016,12]]}},"alternative-id":["1337"],"URL":"https:\/\/doi.org\/10.1186\/s12859-016-1337-6","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,12]]},"article-number":"478"}}