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Ajay, Murcko MA. Computational methods to predict binding free energy in ligand - receptor complexes. of outstanding interest J Med Chem. 38:1995;4953-4967 An excellent review that points out the major current challenges for the development of new scoring functions.
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Bohacek RS, McMartin C. Definition and display of steric, hydrophobic, and hydrogen-bonding properties of ligand binding sites in proteins using Lee and Richards accessible surface: validation of a high resolution graphical tool for drug design. J Med Chem. 35:1992;1671-1684.
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The development of a simple empirical scoring function to estimate the binding constant for a protein - Ligand complex of known three-dimensional structure
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Böhm HJ. The development of a simple empirical scoring function to estimate the binding constant for a protein - ligand complex of known three-dimensional structure. J Comput Aided Mol Des. 8:1994;243-256.
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Horton N, Lewis M. Calculation of the free energy of association for protein complexes. Protein Sci. 1:1992;169-181.
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Affinity and specificity of serine endopeptidase - Protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures
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Krystek S, Stouch T, Novotny J. Affinity and specificity of serine endopeptidase - protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures. J Mol Biol. 234:1993;661-679.
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Effect of conformational flexibility and solvation on receptor - Ligand binding free energies
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A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site
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Holloway MK, Wai JM, Halgren TA. A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site. J Med Chem. 38:1995;305-317.
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Correlation of binding affinities with non-bonded interaction energies of thrombin - Inhibitor complexes
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Grootenhuis PDJ, Van Galen PJM. Correlation of binding affinities with non-bonded interaction energies of thrombin - inhibitor complexes. Acta Crystallogr D - Biol Crystallogr. 51:1995;560-566.
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of special interest. A very interesting paper highlighting the importance of water molecules in protein - ligand interactions.
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Mikol V, Papgeorgiou C, Borer X. The role of water molecules in the structure-based design of (5-hydroxynorvaline)-2-cyclosporin: synthesis, biological activity, and crystallographic analysis with cyclophilin A. of special interest J Med Chem. 38:1995;3361-3367 A very interesting paper highlighting the importance of water molecules in protein - ligand interactions.
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Mikol, V.1
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of special interest. This paper describes the binding of several small molecules to a T4 lysozyme mutant. This type of experimental data is most important to calibrate new computational methods for docking and de novo ligand design.
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Morton A, Matthews BW. Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity. of special interest Biochemistry. 34:1995;8576-8588 This paper describes the binding of several small molecules to a T4 lysozyme mutant. This type of experimental data is most important to calibrate new computational methods for docking and de novo ligand design.
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Morton, A.1
Matthews, B.W.2
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