Zhu J, Fan H, Liu H, Shi Y: Structure-based ligand design for flexible proteins: application of new F-DycoBlock. J Comput Aided Mol Des 2001, 15: 979–996. 10.1023/A:1014817911249
Article
CAS
PubMed
Google Scholar
Jayatilleke PR, Nair AC, Zauhar R, Welsh WJ: Computational studies on HIV-1 protease inhibitors: influence of calculated inhibitor-enzyme binding affinities on the statistical quality of 3D-QSAR CoMFA models. J Med Chem 2000, 43: 4446–4451. 10.1021/jm9905357
Article
CAS
PubMed
Google Scholar
Sham YY, Chu ZT, Tao H, Warshel A: Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease. Proteins 2000, 39: 393–407. 10.1002/(SICI)1097-0134(20000601)39:4<393::AID-PROT120>3.3.CO;2-8
Article
CAS
PubMed
Google Scholar
Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ: Automated Docking Using a Lamarckian Genetic Algorithm and Empirical Binding Free Energy Function. J Comput Chem 1998, 19: 1639–1662. Publisher Full Text 10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B
Article
CAS
Google Scholar
Henry AG, Richard MJ, Michael JES: Modelling Protein Docking using Shape Complimentarity, Electrostatics and Biochemical Information. J Mol Biol 1997, 272: 106–120. 10.1006/jmbi.1997.1203
Article
Google Scholar
Kramer B, Rarey M, Lengauer T: Evaluation of the FlexX incremental construction algorithm for protein-ligand docking proteins. Structure Functions and Genetics 1999, 37: 228–241. Publisher Full Text 10.1002/(SICI)1097-0134(19991101)37:2<228::AID-PROT8>3.0.CO;2-8
CAS
Google Scholar
Verkhivker GM, Rejto PA, Gehlhaar DK, Freer ST: Exploring the energy landscapes of molecular recognition by a genetic algorithm: 10 analysis of the requirements for robust docking of HIV-1 protease and FKBP-12 complexes. Proteins 1996, 25: 342–353. Publisher Full Text 10.1002/(SICI)1097-0134(199607)25:3<342::AID-PROT6>3.3.CO;2-3
Article
CAS
PubMed
Google Scholar
Sham YY, Chu ZT, Tao H, Warshel A: Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease. Proteins 2000, 39: 393–407. 10.1002/(SICI)1097-0134(20000601)39:4<393::AID-PROT120>3.3.CO;2-8
Article
CAS
PubMed
Google Scholar
Pegg SC, Haresco JJ, Kuntz ID: A genetic algorithm for structure-based de novo design. J Comput Aided Mol Des 2001, 15: 911–933. 10.1023/A:1014389729000
Article
CAS
PubMed
Google Scholar
Vakser IA: Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex. Proteins 1997, Suppl 1: 226–230. Publisher Full Text 10.1002/(SICI)1097-0134(1997)1+<226::AID-PROT31>3.3.CO;2-0
Article
CAS
PubMed
Google Scholar
Vakser IA, Matar OG, Lam CF: A systematic study of low-resolution recognition in protein – protein complexes. Proc Natl Acad Sci USA 1999, 96: 8477–8482. 10.1073/pnas.96.15.8477
Article
PubMed Central
CAS
PubMed
Google Scholar
Schaffer L, Verkhivker GM: Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side chain optimization. Proteins 1998, 33: 295–310. 10.1002/(SICI)1097-0134(19981101)33:2<295::AID-PROT12>3.0.CO;2-F
Article
CAS
PubMed
Google Scholar
Verkhivker GM, Rejto PA: A mean field model of ligand-protein interactions: implications for the structural assessment of human immunodeficiency virus type 1 protease complexes and receptor-specific binding. Proc Natl Acad Sci USA 1996, 93: 60–64. 10.1073/pnas.93.1.60
Article
PubMed Central
CAS
PubMed
Google Scholar
Ota N, Agard DA: Binding mode prediction for a flexible ligand in a flexible pocket using multi-conformation simulated annealing pseudo crystallographic refinement. J Mol Biol 2001, 30: 607–617. 10.1006/jmbi.2001.5147
Article
Google Scholar
Betts MJ, Sternberg MJ: An analysis of conformational changes on protein-protein association: implications for predictive docking. Protein Eng 1999, 12: 271–283. 10.1093/protein/12.4.271
Article
CAS
PubMed
Google Scholar
Head RD, Smythe ML, Oprea TI, Waller CL, Green SM, Marshall GR: VALIDATE: A new method for the receptor-based prediction of binding affinities of novel ligands. J Am Chem Soc 1996, 118: 3959–3969. 10.1021/ja9539002
Article
CAS
Google Scholar
Gohlke H, Hendlich M, Klebe G: Knowledge-based Scoring Function to Predict protein-ligand interactions. J Mol Biol 2000, 295: 337–356. 10.1006/jmbi.1999.3371
Article
CAS
PubMed
Google Scholar
Akaho E, Morris GM, Goodsell DS, Wong D, Olson AJ: A study on docking mode of HIV protease and their inhibitors. J Chem Software 2001, 7: 103–114.
Article
CAS
Google Scholar
Klebe G: Recent developments in structure-based drug design. J Mol Med 2000, 78: 269–281. 10.1007/s001090000084
Article
CAS
PubMed
Google Scholar
Schapira M, Totrov M, Abagyan R: Prediction of the binding energy for small molecules, peptides and proteins. J Mol Recognit 1999, 12: 177–190. 10.1002/(SICI)1099-1352(199905/06)12:3<177::AID-JMR451>3.0.CO;2-Z
Article
CAS
PubMed
Google Scholar
Österberg F, Morris GM, Sanner MF, Olson AJ, Goodsell DS: Automated docking to multiple targets structures: Incorporation of protein mobility and structure water heterogeneity in AutoDock. Proteins 2002, 46: 34–40. 10.1002/prot.10028
Article
PubMed
Google Scholar
Harte WE Jr, Swaminathan S, Mansuri MM, Martin JC, Rosenberg IE, Beveridge DL: Domain communication in the dynamical structure of human immunodeficiency virus 1 protease. Proc Natl Acad Sci USA 1990, 87: 8864–8868.
Article
PubMed Central
CAS
PubMed
Google Scholar
Harte WE Jr, Swaminathan S, Beveridge DL: Molecular Dynamics of HIV-1 protease. Protiens 1992, 13: 175–194.
Article
CAS
Google Scholar
York DM, Darden TA, Pedersen LG, Anderson MW: Molecular dynamics simulation of HIV-1 protease in a crystalline environment and in solution. Biochemistry 1993, 32: 1443–1453.
Article
CAS
PubMed
Google Scholar
Navia MA, Fitzgerald PM, McKeever BM, Leu CT, Heimbach JC, Herber WK, Sigal IS, Darke PL, Springer JP: Three dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1. Nature 1989, 337: 615–620. 10.1038/337615a0
Article
CAS
PubMed
Google Scholar
Wlodawer A, Miller M, Jaskolski M, Sathyanarayana BK, Baldwin E, Weber IT, Selk LM, Clawson L, Schneider J, Kent SB: Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease. Science 1989, 245: 616–621.
Article
CAS
PubMed
Google Scholar
Miller M, Schneider J, Sathyanarayana BK, Toth MV, Marshall GR, Clawson L, Selk L, Kent SB, Wlodawer A: Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 Å resolution. Science 1989, 246: 1149–1152.
Article
CAS
PubMed
Google Scholar
Scott WR, Schiffer CA: Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance. Structure Fold Des 2000, 8: 1259–1265. 10.1016/S0969-2126(00)00537-2
Article
CAS
PubMed
Google Scholar
Collins JR, Burt SK, Erickson JW: Flap opening in HIV-1 protease simulated by 'activated' molecular dynamics. Nat Struct Biol 1995, 2: 334–338.
Article
CAS
PubMed
Google Scholar
Collins JR, Burt SK, Erickson JW: Activated dynamics of flap opening in HIV-1 protease. Adv Exp Med Biol 1995, 362: 455–460.
Article
CAS
PubMed
Google Scholar
Rastall RA: Protein, structure and function: Ligand binding.[http://www.fst.rdg.ac.uk/courses/fs916/lect5/lect5.htm]
PDB code: Crystal structures of complexes of a peptidic inhibitor with wild-type and two mutant HIV-1 proteases. Biochemistry 1996, 35: 10627–10633. 10.1021/bi960481s
Article
Google Scholar
PDB code: A check on rational drug design: crystal structure of a complex of human immunodeficiency virus type 1 protease with a novel gamma-turn mimetic inhibitor. J Med Chem 1995, 38: 3246–3252.
Article
Google Scholar
PDB code: Comparative analysis of the X-ray structures of HIV-1 and HIV-2 proteases in complex with CGP 5 a novel pseudosymmetric inhibitor. Structure 3820, 3: 381–389.
Google Scholar
PDB code: Crystal structure of a complex of HIV-1 protease with a dihydroxyethylene-containing inhibitor: comparisons with molecular modeling. Protein Sci 1992, 1: 1061–1072.
Article
Google Scholar
PDB code: Crystal-structure of HIV-1 protease in complex with VX-478, A potent and orally bioavailable inhibitor of the enzyme. J Am Chem Soc 1995, 117: 1181–1189.
Article
Google Scholar
PDB code: X-ray crystallographic studies of a series of penicillin-derived asymmetric inhibitors of HIV-1 protease. Biochemistry 1994, 33: 8417–8427.
Article
Google Scholar
PDB code: 1hvi, 1hvj, 1hvk, 1hvl, Hosur MV, Bhat TN, Kempf DJ, Baldwin ET, Liu BS, Gulnik S, Wideburg NE, Norbeck DW, Appelt K, Erickson JW: Influence of stereochemistry on activity and binding modes for C2 symmetry-based diol inhibitors of HIV-1 protease. J Am Chem Soc 1994, 116: 847.
Article
Google Scholar
PDB code: Structural basis of drug resistance for the V82A mutant of HIV-1 proteinase. Nat Struct Biol 1995, 2: 244–249.
Article
Google Scholar
PDB code: An orally bioavailable HIV-1 protease inhibitor containing an imidazole-derived peptide bond replacement: crystallographic and pharmacokinetic analysis. Biochemistry 1994, 33: 11671–11677.
Article
Google Scholar
PDB code: A novel, picomolar inhibitor of human immunodeficiency virus type 1 protease. J Med Chem 1996, 39: 392–397. 10.1021/jm9507183
Article
Google Scholar
PDB code: Structure-based design of novel HIV protease inhibitors: carboxamide-containing 4-hydroxycoumarins and 4-hydroxy-2-pyrones as potent nonpeptidic inhibitors. J Med Chem 1995, 38: 3624–3637.
Article
Google Scholar
PDB code: Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors. Science 1994, 263: 380–384.
Article
Google Scholar
PDB code: 4phv, Bone R, Vacca JP, Anderson PS, Holloway MK: X-Ray Crystal Structure of the HIV Protease Complex with L-700,417, an Inhibitor with Pseudo C2 Symmetry. J Am Chem Soc 1991, 113: 9382.
Article
Google Scholar
PDB code: The crystal structures at 2.2-A resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations. J Biol Chem 1992, 267: 22770–22778.
Google Scholar
PDB code: Rational design, synthesis, and crystallographic analysis of a hydroxyethylene-based HIV-1 protease inhibitor containing a heterocyclic P1'-P2' amide bond isostere. J Med Chem 1994, 37: 3100–3107.
Article
Google Scholar
PDB code: Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 Å resolution. Science 1989, 246: 1149–1152.
Article
Google Scholar
PDB code: Crystallographic Analysis of a Complex between Human Immunodeficiency Virus Type 1 Protease and Acetyl-Pepstatin at 2.0 Angstroms Resolution. J Biol Chem 1990, 265: 14209–14219.
Google Scholar
PDB code: Structure at 2.5-A resolution of chemically synthesized human immunodeficiency virus type 1 protease complexed with a hydroxyethylene-based inhibitor. Biochemistry 1991, 30: 1600–1609.
Article
Google Scholar
PDB code: Design, Activity and 2.8 Angstroms Crystal Structure of a C2 Symmetric Inhibitor Complexed to HIV-1 Protease. Science 1990, 249: 527–533.
Article
Google Scholar
Stryer L: Biochemistry. WH Freeman and Co., New York 3 Edition 1999, 187–195.
Google Scholar
Creighton TE: Proteins: Structures and Molecular Properties. WH Freeman and Co., New York 2 Edition 1993, 386–389.
Google Scholar
Kale L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips J, Shinozaki A, Varadarajan K, Schulten K: NAMD2: Greater scalability for parallel molecular dynamics. J Comput Phys 1999, 151: 283–312. 10.1006/jcph.1999.6201
Article
CAS
Google Scholar
Brunger AT: X-PLOR version 3.1, A system for X-ray crystallography and NMR. Yale University Press, New Haven, CT 1992.
Google Scholar
Kleywegt GJ, Jones TA: Databases in protein crystallography. Acta Cryst 1998, D54: 1119–1131.
CAS
Google Scholar
Geller M, Miller M, Swanson SM, Maizel J: Analysis of the structure of HIV-1 protease complexed with a hexapeptide inhibitor. Part II: Molecular dynamic studies of the active site region. Proteins 1997, 27: 195–203. 10.1002/(SICI)1097-0134(199702)27:2<195::AID-PROT5>3.3.CO;2-1
Article
CAS
PubMed
Google Scholar
Piana S, Carloni P: Conformational flexibility of the catalytic Asp dyad in HIV-1 protease: an ab initio study on the free enzyme. Proteins: Struct Funct Genet 2000, 39: 26–36. 10.1002/(SICI)1097-0134(20000401)39:1<26::AID-PROT3>3.0.CO;2-N
Article
CAS
Google Scholar
Hyland LJ, Tomaszek TA Jr, Meek TD: Human immunodeficiency virus-1 protease 2. Use of pH rate studies and solvent kinetic isotope effects to elucidate details of chemical mechanism. Biochemistry 1991, 30: 8454–8463.
Article
CAS
PubMed
Google Scholar
Yamazaki T, Nicholson LK, Torchia DA, Wingfield P, Stahl SJ, Kaufman JD, Eyermann CJ, Hodge CN, Lam PYS, Ru Y, Jadhav PK, Chang CH, Weber PC: NMR and X-rays evidence that the HIV protease catalytic aspartyl groups are protonated in the complex formed by the protease and a non-peptide cyclic urea-based inhibitor. J Am Chem Soc 1994, 116: 10791–10792.
Article
CAS
Google Scholar
Grubmuller H, Heymann B, Tavan P: Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force. Science 1996, 271: 997–999.
Article
CAS
PubMed
Google Scholar
Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, DeBolt S III, Ferguson D, Seibel G, Kollman P: AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comp Phys Commun 1995, 91: 1–41. 10.1016/0010-4655(95)00041-D
Article
CAS
Google Scholar
Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, Profeta S, Weiner P: A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc 1984, 106: 765–784.
Article
CAS
Google Scholar
Huang X, Xu L, Luo X, Fan K., Ji R, Pei G, Chen K, Jiang H: Elucidating the inhibiting mode of AHPBA derivatives against HIV-1 protease and building predictive 3D-QSAR models. J Med Chem 2002, 45: 333–343. 10.1021/jm0102710
Article
CAS
PubMed
Google Scholar
Rockey WM, Laederach A, Reilly PJ: Automated docking of α-(1>4)- and α-(1>6)-linked glucosyl trisaccharides and maltopentose 14 into the soybean β-amylase active site. Protein 2000, 40: 299–309. Publisher Full Text 10.1002/(SICI)1097-0134(20000801)40:2<299::AID-PROT100>3.0.CO;2-G
Article
CAS
Google Scholar