title: Bioinformatic approaches for modeling the substrate specificity of HIV-1 protease: an overview.
abstract: HIV-1 protease has a broad and complex substrate specificity, which hitherto has escaped a simple comprehensive definition. This, and the relatively high mutation rate of the retroviral protease, makes it challenging to design effective protease inhibitors. Several attempts have been made during the last two decades to elucidate the enigmatic cleavage specificity of HIV-1 protease and to predict cleavage of novel substrates using bioinformatic analysis methods. This review describes the methods that have been utilized to date to address this important problem and the results achieved. The data sets used are also reviewed and important aspects of these are highlighted.
authors.affiliation: Halmstad University, School of Information Science, Computer & Electrical Engineering, Halmstad, Sweden. thorsteinn.rognvaldsson@ide.hh.se
authors.forename: Thorsteinn
authors.initials: T
authors.lastname: Rögnvaldsson
authors.forename: Liwen
authors.initials: L
authors.lastname: You
authors.forename: Daniel
authors.initials: D
authors.lastname: Garwicz
mesh_terms: D019295:Computational Biology / Q000379:methods* / Q000639:trends*; D015497:HIV-1 / Q000201:enzymology*; D006801:Humans; D008956:Models, Chemical; D010447:Peptide Hydrolases / Q000737:chemistry* / Q000378:metabolism*; D013379:Substrate Specificity / Q000502:physiology
chemical_list: D010447:Peptide Hydrolases