1: Johnson EC, Malito E, Shen Y, Pentelute B, Rich D, Florián J, Tang WJ, Kent SB. Insights from atomic-resolution X-ray structures of chemically synthesized HIV-1 protease in complex with inhibitors. J Mol Biol. 2007 Oct 26;373(3):573-86. Epub 2007 Aug 2. PubMed PMID: 17869270; PubMed Central PMCID: PMC2094697.
2: Cieplak P. Some computational aspects of theoretical anti-HIV drug design. Acta Pol Pharm. 2000 Nov;57 Suppl:33-6. PubMed PMID: 11293258.
3: Popov ME, Kashparov IV, Rumsh LD, Popov EM. [Mechanism of aspartyl proteinase action. VII. Noncovalent complexes of HIV-1 aspartyl proteinase with substrate and substrate-like inhibitors]. Bioorg Khim. 1999 Dec;25(12):911-22. Russian. PubMed PMID: 10734551.
4: Popov ME, Kashparov IV, Rumsh LD, Popov EM. [Mechanism of action of aspartic proteases. III. Conformational characteristics of HIV-1 protease inhibitor JG-365]. Bioorg Khim. 1999 Jun;25(6):418-22. Russian. PubMed PMID: 10505229.
5: Martin JL, Begun J, Schindeler A, Wickramasinghe WA, Alewood D, Alewood PF, Bergman DA, Brinkworth RI, Abbenante G, March DR, Reid RC, Fairlie DP. Molecular recognition of macrocyclic peptidomimetic inhibitors by HIV-1 protease. Biochemistry. 1999 Jun 22;38(25):7978-88. PubMed PMID: 10387041.
6: Ding YS, Rich DH, Ikeda RA. Substrates and inhibitors of human T-cell leukemia virus type I protease. Biochemistry. 1998 Dec 15;37(50):17514-8. PubMed PMID: 9860866.
7: Lee CY, Yang PK, Tzou WS, Hwang MJ. Estimates of relative binding free energies for HIV protease inhibitors using different levels of approximations. Protein Eng. 1998 Jun;11(6):429-37. PubMed PMID: 9725621.
8: Mestres J, Rohrer DC, Maggiora GM. A molecular field-based similarity approach to pharmacophoric pattern recognition. J Mol Graph Model. 1997 Apr;15(2):114-21, 103-6. PubMed PMID: 9385558.
9: Laskowski RA, Thornton JM, Humblet C, Singh J. X-SITE: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins. J Mol Biol. 1996 May 31;259(1):175-201. PubMed PMID: 8648645.
10: Verkhivker GM. Empirical free energy calculations of human immunodeficiency virus type 1 protease crystallographic complexes. II. Knowledge-based ligand-protein interaction potentials applied to thermodynamic analysis of hydrophobic mutations. Pac Symp Biocomput. 1996:638-52. PubMed PMID: 9390264.
11: Verkhivker G, Appelt K, Freer ST, Villafranca JE. Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity. Protein Eng. 1995 Jul;8(7):677-91. PubMed PMID: 8577696.
12: Chen X, Tropsha A. Relative binding free energies of peptide inhibitors of HIV-1 protease: the influence of the active site protonation state. J Med Chem. 1995 Jan 6;38(1):42-8. PubMed PMID: 7837238.
13: Baca M, Kent SB. Catalytic contribution of flap-substrate hydrogen bonds in "HIV-1 protease" explored by chemical synthesis. Proc Natl Acad Sci U S A. 1993 Dec 15;90(24):11638-42. PubMed PMID: 8265601; PubMed Central PMCID: PMC48039.
14: Fujisawa Y, Kakinuma A. [HIV protease inhibitors]. Tanpakushitsu Kakusan Koso. 1993 Aug;38(11):2012-30. Review. Japanese. PubMed PMID: 8210441.
15: Rich DH, Prasad JV, Sun CQ, Green J, Mueller R, Houseman K, MacKenzie D, Malkovsky M. New hydroxyethylamine HIV protease inhibitors that suppress viral replication. J Med Chem. 1992 Oct 16;35(21):3803-12. PubMed PMID: 1433192.
16: Tropsha A, Hermans J. Application of free energy simulations to the binding of a transition-state-analogue inhibitor to HIV protease. Protein Eng. 1992 Jan;5(1):29-33. PubMed PMID: 1631042.
17: Ferguson DM, Radmer RJ, Kollman PA. Determination of the relative binding free energies of peptide inhibitors to the HIV-1 protease. J Med Chem. 1991 Aug;34(8):2654-9. PubMed PMID: 1652028.
18: Swain AL, Gustchina A, Wlodawer A. Comparison of three inhibitor complexes of human immunodeficiency virus protease. Adv Exp Med Biol. 1991;306:433-41. PubMed PMID: 1812740.
19: Swain AL, Miller MM, Green J, Rich DH, Schneider J, Kent SB, Wlodawer A. X-ray crystallographic structure of a complex between a synthetic protease of human immunodeficiency virus 1 and a substrate-based hydroxyethylamine inhibitor. Proc Natl Acad Sci U S A. 1990 Nov;87(22):8805-9. PubMed PMID: 2247451; PubMed Central PMCID: PMC55048.