Structure-based prediction of binding affinities and molecular design of peptide ligands.

[1]  V. Hilser,et al.  The magnitude of the backbone conformational entropy change in protein folding , 1996, Proteins.

[2]  A. Wlodawer,et al.  [14]Subsite preferences of retroviral proteinases , 1994 .

[3]  R. Bruccoleri,et al.  On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5. , 1989, Biochemistry.

[4]  S. Gulnik,et al.  Dissection of the pH dependence of inhibitor binding energetics for an aspartic protease: direct measurement of the protonation states of the catalytic aspartic acid residues. , 1997, Biochemistry.

[5]  I. Luque,et al.  Structure‐based thermodynamic design of peptide ligands: Application to peptide inhibitors of the aspartic protease endothiapepsin , 1998, Proteins.

[6]  M Karplus,et al.  Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics. , 1995, Advances in protein chemistry.

[7]  K. P. Murphy,et al.  Entropy in biological binding processes: Estimation of translational entropy loss , 1994, Proteins.

[8]  M. Doyle,et al.  Human immunodeficiency virus protease ligand specificity conferred by residues outside of the active site cavity. , 1996, Biochemistry.

[9]  D. Xie,et al.  Molecular basis of cooperativity in protein folding. V. Thermodynamic and structural conditions for the stabilization of compact denatured states , 1994, Proteins.

[10]  V. Hilser,et al.  Structure-based statistical thermodynamic analysis of T4 lysozyme mutants: structural mapping of cooperative interactions. , 1997, Biophysical chemistry.

[11]  K. P. Murphy,et al.  Molecular basis of co-operativity in protein folding. , 1992, Journal of molecular biology.

[12]  K. P. Murphy,et al.  Thermodynamics of structural stability and cooperative folding behavior in proteins. , 1992, Advances in protein chemistry.

[13]  D. Xie,et al.  Structure based prediction of protein folding intermediates. , 1994, Journal of molecular biology.

[14]  V. Hilser,et al.  The enthalpy change in protein folding and binding: Refinement of parameters for structure‐based calculations , 1996, Proteins.

[15]  T. Blundell,et al.  X-ray analyses of aspartic proteinases. The three-dimensional structure at 2.1 A resolution of endothiapepsin. , 1994, Journal of molecular biology.

[16]  Vincenzo Mollica,et al.  Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution , 1981 .

[17]  V. Hilser,et al.  Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors. , 1996, Journal of molecular biology.

[18]  V. Hilser,et al.  The heat capacity of proteins , 1995, Proteins.

[19]  D Norbeck,et al.  Characterization of human immunodeficiency virus type 1 variants with increased resistance to a C2-symmetric protease inhibitor , 1994, Journal of virology.

[20]  A. Wlodawer,et al.  Different requirements for productive interaction between the active site of HIV-1 proteinase and substrates containing -hydrophobic*hydrophobic- or -aromatic*pro- cleavage sites. , 1992, Biochemistry.

[21]  M. Gilson,et al.  The statistical-thermodynamic basis for computation of binding affinities: a critical review. , 1997, Biophysical journal.

[22]  E. Freire.  Structural thermodynamics: prediction of protein stability and protein binding affinities. , 1993, Archives of biochemistry and biophysics.

[23]  John W. Erickson,et al.  Structural basis of drug resistance for the V82A mutant of HIV-1 proteinase , 1995, Nature Structural Biology.

[24]  R. Lumry,et al.  Enthalpy–entropy compensation phenomena in water solutions of proteins and small molecules: A ubiquitous properly of water , 1970, Biopolymers.

[25]  K. P. Murphy,et al.  Molecular basis of co-operativity in protein folding. III. Structural identification of cooperative folding units and folding intermediates. , 1992, Journal of molecular biology.

[26]  Philip R. Johnson,et al.  Antibodies to the putative SIV infection‐enhancing domain diminish beneficial effects of an SIV gp160 vaccine in rhesus macaques , 1995, AIDS.

[27]  J. Condra,et al.  In vivo emergence of HIV-1 variants resistant to multiple protease inhibitors , 1995, Nature.

[28]  G. Marshall,et al.  Calibration of effective van der Waals atomic contact radii for proteins and peptides , 1987, Proteins.

[29]  A. Wlodawer,et al.  Structure-based inhibitors of HIV-1 protease. , 1993, Annual review of biochemistry.

[30]  Ian M. Brereton,et al.  Ionization states of the catalytic residues in HIV-1 protease , 1996, Nature Structural Biology.

[31]  R. Poljak,et al.  The three-dimensional structure of the aspartyl protease from the HIV-1 isolate BRU. , 1991, Biochimie.

[32]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[33]  B. García-Moreno,et al.  Probing structural and physical basis of protein energetics linked to protons and salt. , 1995, Methods in enzymology.

[34]  V. Hilser,et al.  Predicting the equilibrium protein folding pathway: Structure‐based analysis of staphylococcal nuclease , 1997, Proteins.

[35]  R. DesJarlais,et al.  An orally bioavailable HIV-1 protease inhibitor containing an imidazole-derived peptide bond replacement: crystallographic and pharmacokinetic analysis. , 1994, Biochemistry.

[36]  A Wlodawer,et al.  Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution. , 1989, Science.

[37]  M. Levitt,et al.  Conformation of amino acid side-chains in proteins. , 1978, Journal of molecular biology.

[38]  S Foundling,et al.  Effect of point mutations on the kinetics and the inhibition of human immunodeficiency virus type 1 protease: relationship to drug resistance. , 1995, Biochemistry.

[39]  E. Freire,et al.  Thermodynamic mapping of the inhibitor site of the aspartic protease endothiapepsin. , 1995, Journal of molecular biology.

[40]  I. Luque,et al.  Structure-based thermodynamic scale of alpha-helix propensities in amino acids. , 1996, Biochemistry.

[41]  S Foundling,et al.  Crystal structures of complexes of a peptidic inhibitor with wild-type and two mutant HIV-1 proteases. , 1996, Biochemistry.

[42]  L M Amzel,et al.  Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation , 1994, Proteins.

[43]  I. Luque,et al.  Structure-based thermodynamic analysis of HIV-1 protease inhibitors. , 1997, Biochemistry.

[44]  T. Blundell,et al.  X-ray-crystallographic studies of complexes of pepstatin A and a statine-containing human renin inhibitor with endothiapepsin. , 1993, The Biochemical journal.

[45]  M. Murcko,et al.  Crystal Structure of HIV-1 Protease in Complex with Vx-478, a Potent and Orally Bioavailable Inhibitor of the Enzyme , 1995 .

[46]  G D Rose,et al.  Modeling unfolded states of peptides and proteins. , 1995, Biochemistry.

[47]  G. Fasman,et al.  Structure and stability of biological macromolecules , 1969 .

[48]  T. Meek,et al.  Human immunodeficiency virus-1 protease. 2. Use of pH rate studies and solvent kinetic isotope effects to elucidate details of chemical mechanism. , 1991, Biochemistry.

[49]  E. Lattman,et al.  Experimental measurement of the effective dielectric in the hydrophobic core of a protein. , 1997, Biophysical chemistry.

[50]  M. Adams,et al.  Biocatalysis at Extreme Temperatures: Enzyme Systems Near and Above 100 °C , 1992 .

[51]  K. P. Murphy,et al.  Structural energetics of peptide recognition: Angiotensin II/antibody binding , 1993, Proteins.

[52]  T. Yamazaki,et al.  Solution NMR evidence that the HIV-1 protease catalytic aspartyl groups have different ionization states in the complex formed with the asymmetric drug KNI-272. , 1996, Biochemistry.