Reviews in Computational Chemistry Volume 18

References 85
172. C. Lemmen, T. Lengauer, and G. Klebe, J. Med. Chem., 41, 4502 (1998). FlexS: A Method for
Fast Flexible Ligand Superposition.
173. C. Lemmen, A. Zien, R. Zimmer, and T. Lengauer, Abstracts of the Pacific Symposium on
Biocomputing, Big Island, Hawaii, January 4–9, 1999, pp. 482–493. Application of Parameter
Optimization to Molecular Comparison.
174. G. R. Desiraju and T. Steiner, The Weak Hydrogen Bond in Chemistry and Biology, Oxford
University Press, Oxford, UK, 1999.
175. G. Parkinson, A. Gunasekera, J. Vojtechovsky, X. Zhang, T. Kunkel, H. Berman, and R. H.
Ebright, Nature Struct. Biol., 3, 837 (1996). Aromatic Hydrogen Bond in Sequence-Specific
Protein DNA Recognition.
176. J. P. Gallivan and D. A. Dougherty, Proc. Natl. Acad. Sci. U.S.A., 96, 9459 (1999). Cation–p
Interactions in Structural Biology.
177. J. P. Gallivan and D. A. Dougherty, J. Am. Chem. Soc., 122, 870 (2000). A Computational
Study of Cation–p Interactions vs. Salt Bridges in Aqueous Media: Implications for Protein
Engineering.
178. G. B. McGaughey, M. Gagné, and A. K. Rappé, J. Biol. Chem., 273, 15458 (1998). p-Stacking
Interactions.
179. C. Chipot, R. Jaffe, B. Maigret, D. A. Pearlman, and P. A. Kollman, J. Am. Chem. Soc., 118,
11217 (1996). The Benzene Dimer: A Good Model for p–p Interactions in Proteins? A
Comparison Between the Benzene and the Toluene Dimers in the Gas Phase and in Aqueous
Solution.
180. T. G. Davies, R. E. Hubbard, and J. R. H. Tame, Protein Sci., 8, 1432 (1999). Relating
Structure to Thermodynamics: The Crystal Structures and Binding Affinity of Eight OppA-
Peptide Complexes.
181. G. Klebe, F. Dullweber, and H.-J. Boehm, in Drug-Receptor Thermodynamics: Introduction
and Applications, R. B. Raffa, Ed., Wiley, Chichester, UK, 2001, pp. 83–103. Thermodynamic
Models of Drug-Receptor Interactions: A General Introduction.
182. S. Ha, R. Andreani, A. Robbins, and I. Muegge, J. Comput.-Aided Mol. Design, 14, 435
(2000). Evaluation of Docking/Scoring Approaches: A Comparative Study Based on MMP3
Inhibitors.
183. I. Massova and P. A. Kollman, Perspect. Drug Discovery Design, 18, 113 (2000). Combined
Molecular Mechanical and Continuum Solvent Approach (MM-PBSA/GBSA) to Predict
Ligand Binding.
184. B. Kuhn and P. A. Kollman, J. Med. Chem., 43, 3786 (2000). Binding of a Diverse Set
of Ligands to Avidin and Streptavidin: An Accurate Quantitative Prediction of Their
Relative Affinities by a Combination of Molecular Mechanics and Continuum Solvent
Models.
185. N. Froloff, A. Windemuth, and B. Honig, Protein Sci., 6, 1293 (1997). On the Calculation of
Binding Free Energies Using Continuum Methods: Application to MHC Class I Protein–
Peptide Interactions.
186. J. Shen, J. Med. Chem., 40, 2953 (1997). A Theoretical Investigation of Tight-Binding
Thermolysin Inhibitors.
187. C. J. Woods, M. A. King, and J. W. Essex, J. Comput.-Aided Mol. Design, 15, 129 (2001). The
Configurational Dependence of Binding Free Energies: A Poisson–Boltzmann Study of
Neuraminidase Inhibitors.
188. G. Archontis, T. Simonson, and M. Karplus, J. Mol. Biol., 306, 307 (2001). Binding Free
Energies and Free Energy Components from Molecular Dynamics and Poisson–Boltzmann
Calculations. Application to Amino Acid Recognition by Aspartyl–tRNA Synthetase.
189. A. R. Leach, J. Mol. Biol., 235, 345 (1994). Ligand Docking to Proteins With Discrete Side-
Chain Flexibility.
190. R. M. A. Knegtel, I. D. Kuntz, and C. M. Oshiro, J. Mol. Biol., 266, 424 (1997). Molecular
Docking to Ensembles of Protein Structures.