DOI: 10.31038/AMM.2020112

HIV Protease Cleavage Sites

About 25 years ago a very important paper on prediction of human immunodeficiency virus protease cleavage sites in proteins [1] was published.

Ever since then, a series of papers for predicting HIV protease cleavage sites in proteins have been stimulated (see, e.g., [2-36]). All these papers are very useful for developing new drugs against human immunodeficiency.

References

1. C. Chou (1996) Review: Prediction of human immunodeficiency virus protease cleavage sites in proteins, Anal. Biochem 233 1-14.[crossref]
2. D. Cai, K.C. Chou (1998) Artificial neural network model for HIV protease cleavage sites in proteins, Advances in Engineering Software, 29 119-128. [crossref]
3. D. Cai, H. Yu, K.C. Chou (1998) Using neural network for prediction of HIV protease cleavage sites in proteins, J. Protein Chem 17 607-615. [crossref]
4. W. Cameron, A.J. Japour, Y. Xu, A. Hsu, J. Mellors, C. Farthing, C. Cohen, D. Poretz, M. Markowitz, S. Follansbee, J.B. Angel, D. McMahon, D. Ho, V. Devanarayan, R. Rode, M. Salgo, D.J. Kempf, R. Granneman, J.M. Leonard, E. Sun, et al (1999) Ritonavir and saquinavir combination therapy for the treatment of HIV infection, Aids, 13 213-224. [crossref]
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8. J. Root, M.S. Kay, P.S. Kim (2001) Protein design of an HIV-1 entry inhibitor, Science, 291 884-888. [crossref]
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10. A. Bewley, J.M. Louis, R. Ghirlando, G.M. Clore (2002) Design of a novel peptide inhibitor of HIV fusion that disrupts the internal trimeric coiled-coil of gp41, J. Biol. Chem 277 14238-14245. [crossref]
11. D. Cai, X.J. Liu, X.B. Xu, K.C. Chou (2002) Support Vector Machines for predicting HIV protease cleavage sites in protein, J. Comput. Chem 23 267-274.
12. Fellay, C. Marzolini, E.R. Meaden, D.J. Back, T. Buclin, J.P. Chave, L.A. Decosterd, H. Furrer, M. Opravil, G. Pantaleo, D. Retelska, L. Ruiz, A.H. Schinkel, P. Vernazza, C.B. Eap, A. Telenti, et al (2002) Response to antiretroviral treatment in HIV-1-infected individuals with allelic variants of the multidrug resistance transporter 1: a pharmacogenetics study, Lancet, 359 30-36. [crossref]
13. Rognvaldsson, L. You (2004) Why neural networks should not be used for HIV-1 protease cleavage site prediction, Bioinformatics, 20 1702-1709. [crossref]
14. R. Yang, A.R. Dalby, J. Qiu (2004) Mining HIV protease cleavage data using genetic programming with a sum-product function, Bioinformatics, 20 3398-3405. [crossref]
15. Sirois, T. Sing, K.C. Chou (2005) Review: HIV-1 gp120 V3 loop for structure-based drug design, Current Protein and Peptide Science, 6 413-422. [crossref]
16. Sirois, C.M. Tsoukas, K.C. Chou, D.Q. Wei, C. Boucher, G.E. Hatzakis, et al (2005) Selection of Molecular Descriptors with Artificial Intelligence for the Understanding of HIV-1 Protease Peptidomimetic Inhibitors-activity, Medicinal Chemistry, 1 173-184.
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18. N. Gao, D.Q. Wei, Y. Li, H. Gao, W.R. Xu, A.X. Li, K.C. Chou, et al (2007) Agaritine and its derivatives are potential inhibitors against HIV proteases, Medicinal Chemistry, 3 221-226. [crossref]
19. Kontijevskis, J.E. Wikberg, J. Komorowski (2007) Computational proteomics analysis of HIV-1 protease interactome, Proteins, 68 305-312. [crossref]
20. Rognvaldsson, L. You, D. Garwicz (2007) Bioinformatic approaches for modeling the substrate specificity of HIV-1 protease: an overview, Expert Rev Mol Diagn, 7 435-451.
21. Sirois, M. Touaibia, K.C. Chou, R. Roy (2007) Review: Glycosylation of HIV-1 gp120 V3 loop: towards the rational design of a synthetic carbohydrate vaccine, Current Medicinal Chemistry, 14 3232-3242.
22. Kim, Y. Zhang, Y.S. Heo, H.B. Oh, S.S. Chen (2008) Specificity rule discovery in HIV-1 protease cleavage site analysis, Comput Biol Chem, 32 71-78. [crossref]
23. Nanni, A. Lumini (2008) Using ensemble of classifiers for predicting HIV protease cleavage sites in proteins, Amino Acids, Accepted Mar-27-2008. [crossref]
24. B. Shen, K.C. Chou (2008) HIVcleave: a web-server for predicting HIV protease cleavage sites in proteins, Anal. Biochem 375 388-390. [crossref]
25. M. Andrianov (2009) Immunophilins and HIV-1 V3 loop for structure-based anti-AIDS drug design, J. Biomol. Struct. Dyn 26 445-454. [crossref]
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27. Nanni, A. Lumini (2009) A Further Step Toward an Optimal Ensemble of Classifiers for Peptide Classification, a Case Study: HIV Protease, Protein & Peptide Letters, 16 163-167. [crossref]
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29. H. Wong, T.B. Ng, Y. Jiang, F. Liu, S.C. Sze, K.Y. Zhang (2010) Purification and characterization of a Laccase with inhibitory activity toward HIV-1 reverse transcriptase and tumor cells from an edible mushroom (Pleurotus cornucopiae), Protein & Peptide Letters, 17 1040-1047.
30. Huang, Z. Xu, L. Chen, Y.D. Cai, X. Kong (2011) Computational Analysis of HIV-1 Resistance Based on Gene Expression Profiles and the Virus-Host Interaction Network, PLoS ONE, 6 e17291. [crossref]
31. Maria Velasco, A. Becerra, R. Hernandez-Morales, L. Delaye, M.E. Jimenez-Corona, S. Ponce-de-Leon, A. Lazcano, et al (2013) Low complexity regions (LCRs) contribute to the hypervariability of the HIV-1 gp120 protein, J. Theor. Biol 338 80-86.
32. Dev, D. Park, Q. Fu, J. Chen, H.J. Ha, F. Ghantous, T. Herrmann, W. Chang, Z. Liu, G. Frey, M.S. Seaman, B. Chen, J.J. Chou, et al (2016) Structural Basis for Membrane Anchoring of HIV-1 Envelope Spike, Science 353 172-175. [crossref]
33. Chen, J.J. Chou (2017) Structure of the transmembrane domain of HIV-1 envelope glycoprotein, FEBS J, 284 1171-1177. [crossref]
34. Piai, J. Dev, Q. Fu, J.J. Chou (2017) Stability and Water Accessibility of the Trimeric Membrane Anchors of the HIV-1 Envelope Spikes, J. Am. Chem. Soc 139 18432-18435. [crossref]
35. Fu, M.M. Shaik, Y. Cai, F. Ghantous, A. Piai, H. Peng, S. Rits-Volloch, Z. Liu, S.C. Harrison, M.S. Seaman, B. Chen, J.J. Chou, et al (2018) Structure of the membrane proximal external region of HIV-1 envelope glycoprotein, Proc. Natl. Acad. Sci. U. S. A 115 E8892-E8899. [crossref]
36. J. Mei, J. Zhao (2018) Prediction of HIV-1 and HIV-2 proteins by using Chou’s pseudo amino acid compositions and different classifiers, Sci Rep, 8 2359.