Thermodynamic penalty arising from burial of a ligand polar group within a hydrophobic pocket of a protein receptor.
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Jirí Cerný | Agnieszka Bronowska | Jirí Vondrásek | S. Phillips | J. Vondrášek | S. Homans | J. Černý | R. Bingham | A. Bronowska | Steve W Homans | Elizabeth Barratt | Richard Bingham | Simon Phillips | E. Barratt
[1] Ronald M. Levy,et al. Thermodynamic Decomposition of Hydration Free Energies by Computer Simulation: Application to Amines, Oxides, and Sulfides , 1997 .
[2] Vincenzo Mollica,et al. Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution , 1981 .
[3] J D Dunitz,et al. Win some, lose some: enthalpy-entropy compensation in weak intermolecular interactions. , 1995, Chemistry & biology.
[4] Milos V Novotny,et al. Thermodynamic analysis of binding between mouse major urinary protein-I and the pheromone 2-sec-butyl-4,5-dihydrothiazole. , 2003, Biochemistry.
[5] C. Pace,et al. The Contribution of Polar Group Burial to Protein Stability Is Strongly Context-dependent* , 2003, Journal of Biological Chemistry.
[6] Energetic contribution of side chain hydrogen bonding to the stability of staphylococcal nuclease. , 1995, Biochemistry.
[7] J. Zou,et al. Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.
[8] S. Homans,et al. Optimization of tether length in nonglycosidically linked bivalent ligands that target sites 2 and 1 of a Shiga-like toxin. , 2003, Journal of the American Chemical Society.
[9] S. Homans,et al. Dissecting the cholera toxin-ganglioside GM1 interaction by isothermal titration calorimetry. , 2004, Journal of the American Chemical Society.
[10] Anastassis Perrakis,et al. Developments in the CCP4 molecular-graphics project. , 2004, Acta crystallographica. Section D, Biological crystallography.
[11] Jirí Cerný,et al. Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations , 2007, J. Comput. Chem..
[12] Everett L. Shock,et al. Thermodynamic functions of hydration of hydrocarbons at 298.15 K and 0.1 MPa , 2000 .
[13] David E. Smith,et al. Free energy, entropy, and internal energy of hydrophobic interactions: Computer simulations , 1993 .
[14] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[15] G. Bodenhausen,et al. Thermodynamics of binding of 2-methoxy-3-isopropylpyrazine and 2-methoxy-3-isobutylpyrazine to the major urinary protein. , 2004, Journal of the American Chemical Society.
[16] G. Scuseria,et al. Climbing the density functional ladder: nonempirical meta-generalized gradient approximation designed for molecules and solids. , 2003, Physical review letters.
[17] S. Jackson,et al. Context-dependent nature of destabilizing mutations on the stability of FKBP12. , 1998, Biochemistry.
[18] George I Makhatadze,et al. Thermodynamic consequences of burial of polar and non-polar amino acid residues in the protein interior. , 2002, Journal of molecular biology.
[19] Charles A Laughton,et al. Strong solute-solute dispersive interactions in a protein-ligand complex. , 2005, Journal of the American Chemical Society.
[20] Y. Yamagata,et al. Contribution of polar groups in the interior of a protein to the conformational stability. , 2001, Biochemistry.
[21] P. Kollman,et al. Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation , 1993 .
[22] B. Sigurskjold,et al. Exact analysis of competition ligand binding by displacement isothermal titration calorimetry. , 2000, Analytical biochemistry.
[23] A. Klamt,et al. COSMO : a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient , 1993 .
[24] R J Read,et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.
[25] Hans W. Horn,et al. ELECTRONIC STRUCTURE CALCULATIONS ON WORKSTATION COMPUTERS: THE PROGRAM SYSTEM TURBOMOLE , 1989 .
[26] Charles A Laughton,et al. Van der Waals interactions dominate ligand-protein association in a protein binding site occluded from solvent water. , 2005, Journal of the American Chemical Society.
[27] H. Berendsen,et al. Molecular dynamics with coupling to an external bath , 1984 .
[28] A. Fersht,et al. Effect of cavity-creating mutations in the hydrophobic core of chymotrypsin inhibitor 2. , 1993, Biochemistry.
[29] J F Brandts,et al. Rapid measurement of binding constants and heats of binding using a new titration calorimeter. , 1989, Analytical biochemistry.
[30] F. J. Luque,et al. Classical molecular interaction potentials: Improved setup procedure in molecular dynamics simulations of proteins , 2001, Proteins.
[31] B. Matthews,et al. Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme , 2001, Protein science : a publication of the Protein Society.
[32] Collaborative Computational,et al. The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.
[33] G. Ciccotti,et al. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .
[34] B. Matthews,et al. Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala-->Ser and Val-->Thr substitutions in T4 lysozyme. , 1993, Biochemistry.
[35] Marco Häser,et al. Auxiliary basis sets to approximate Coulomb potentials , 1995 .