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1
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0030960230
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Structure-based drug design: Computational advances
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Marrone TJ, Briggs JM, McCammon JA: Structure-based drug design: computational advances. Annu Rev Pharmacol Toxicol 1997, 37:71-90. A well organized introduction to computational methods applicable to each stage of the drug design process. Particularly helpful is a section summarizing various programs for building lead compounds from molecular fragments.
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Annu Rev Pharmacol Toxicol
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Marrone, T.J.1
Briggs, J.M.2
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2
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0030474049
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What can we learn from molecular recognition in protein-ligand complexes for the design of new drugs?
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Böhm H-J, Klebe G: What can we learn from molecular recognition in protein-ligand complexes for the design of new drugs? Angew Chem Int Ed 1996, 35:2588-2614. A review of typical protein-ligand interactions and binding modes that may be exploited in drug design. In the discussion of computational methods, approaches to lead discovery are emphasized.
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Angew Chem Int Ed
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Böhm, H.-J.1
Klebe, G.2
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3
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0029623184
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Computational methods to predict binding free energy in ligand-receptor complexes
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Ajay, Murcko MA: Computational methods to predict binding free energy in ligand-receptor complexes. J Med Chem 1995, 38:4953-4967.
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J Med Chem
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Ajay1
Murcko, M.A.2
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4
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0346633937
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Viability of molecular modeling with Pentium-based PCs
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Tirado-Rives J, Jorgensen WL: Viability of molecular modeling with Pentium-based PCs. J Comput Chem 1996, 117:1385-1386.
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J Comput Chem
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Tirado-Rives, J.1
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5
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2542564912
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Advances and continuing challenges in achieving realistic and predictive simulations of the properties of organic and biological molecules
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Kollman PA: Advances and continuing challenges in achieving realistic and predictive simulations of the properties of organic and biological molecules. Accounts Chem Res 1996, 29:461-469.
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Accounts Chem Res
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Kollman, P.A.1
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6
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0029912748
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Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
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Jorgensen WL, Maxwell DS, Tirado-Rives J: Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 1996, 118:11225-11236.
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(1996)
J Am Chem Soc
, vol.118
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Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
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7
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0030745939
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Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assessment of empirical force fields
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Beachy MD, Chasman D, Murphy RB, Halgren TA, Friesner RA: Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assessment of empirical force fields. J Am Chem Soc 1997, 119:5908-5920. The energies of alanine dipeptide and tetrapeptide conformations were determined quantum mechanically and form the basis for comparison of 20 widely-used molecular mechanics force field potential functions, including those available in the software package, Macromodel. The level of discussion may be daunting for those new to computational chemistry, but this paper represents a significant step in side-by-side comparison of force fields. The few that perform consistently well for this important application are noted, and the benchmark structures are available on the World Wide Web (http://www.chem.columbia.edu/beach/structures.html) for further use in force field development.
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J Am Chem Soc
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Beachy, M.D.1
Chasman, D.2
Murphy, R.B.3
Halgren, T.A.4
Friesner, R.A.5
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8
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0000843589
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Performance of the AMBER94, MMFF94, and OPLS-AA force fields for modeling organic liquids
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Kaminski G, Jorgensen WL: Performance of the AMBER94, MMFF94, and OPLS-AA force fields for modeling organic liquids. J Phys Chem 1996, 100:18010-18013.
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(1996)
J Phys Chem
, vol.100
, pp. 18010-18013
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Kaminski, G.1
Jorgensen, W.L.2
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9
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0003241140
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Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy
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Helms V, Wade RC: Free energies of hydration from thermodynamic integration: comparison of molecular mechanics force fields and evaluation of calculation accuracy. J Comput Chem 1997, 18:449-462.
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J Comput Chem
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Helms, V.1
Wade, R.C.2
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10
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0030180875
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New model for calculation of solvation free energies: Correction of self-consistent reaction field continuum dielectric theory for short range hydrogen-bonding effects
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Marten B, Kim K, Cortis C, Friesner RA, Murphy RB, Ringnalda MN, Sitkoff D, Honig B: New model for calculation of solvation free energies: correction of self-consistent reaction field continuum dielectric theory for short range hydrogen-bonding effects. J Phys Chem 1996, 100:11775-11788.
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J Phys Chem
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Marten, B.1
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Ringnalda, M.N.6
Sitkoff, D.7
Honig, B.8
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11
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0000785131
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A re-examination of the hydrophobic effect: Exploring the role of the solvent model in computing the methane-methane potential of mean force
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Young WS, Brooks CL III: A re-examination of the hydrophobic effect: exploring the role of the solvent model in computing the methane-methane potential of mean force. J Chem Phys 1997, 106:9265-9269. This self-association of methane in water is often studied to gain insight into protein folding via the 'hydrophobic effect'. While a current trend in force field calculations is the inclusion of explicit electronic polarization, this comparison study of popular three point (TIP3P), four point (TIP4P) and polarizable TIP4P water models yielded similar potentials of mean force with both competitive contact and solvent-separated minima. It was concluded that explicit polarization does not significantly effect the dimerization of methane; however, the structure of the solvent did influence the relative populations of solvent-separated versus contact methane pairs.
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(1997)
J Chem Phys
, vol.106
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Young, W.S.1
Brooks C.L. III2
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0347637403
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Computational studies of molecular recognition from alkane dimers to protein-ligand complexes
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Edited by Seddon KR, Zaworotko MJ. The Netherlands: Kluwer Academic Publishers; in press
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Jorgensen WL, Duffy EM, Essex JW, Severance DL, Blake JF, McDonald NA, Tirado-Rives J: Computational studies of molecular recognition from alkane dimers to protein-ligand complexes. In Crystal Engineering: The Design and Application of Functional Solids. Edited by Seddon KR, Zaworotko MJ. The Netherlands: Kluwer Academic Publishers; 1997, in press.
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(1997)
Crystal Engineering: The Design and Application of Functional Solids
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Jorgensen, W.L.1
Duffy, E.M.2
Essex, J.W.3
Severance, D.L.4
Blake, J.F.5
McDonald, N.A.6
Tirado-Rives, J.7
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13
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0029745052
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Cation-π interactions in aromatics of biological and medicinal interest: Electrostatic potential surfaces as a useful qualitative guide
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Mecozzi S, West AP Jr, Dougherty DA: Cation-π interactions in aromatics of biological and medicinal interest: electrostatic potential surfaces as a useful qualitative guide. Proc Natl Acad Sci USA 1996, 93:10566-10571. Interactions between sodium ions and various substituted aromatics and heterocycles are presented quantitatively and qualitatively as electrostatic potential surface maps. Electrostatics rather than polarizablity is found to govern the structure and energetics of the complexes. Visualization of these potential surface maps may be a useful predictive tool for drug design.
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Proc Natl Acad Sci USA
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Mecozzi, S.1
West A.P., Jr.2
Dougherty, D.A.3
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14
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0030001537
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Benzene dimer: A good model for π-πinteractions in proteins? A comparison between the benzene and the toluene dimers in the gas phase and in an aqueous solution
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Chipot C, Jaffe R, Maigret B, Pearlman DA, Kollman PA: Benzene dimer: a good model for π-πinteractions in proteins? A comparison between the benzene and the toluene dimers in the gas phase and in an aqueous solution. J Am Chem Soc 1996, 118:11217-11224.
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J Am Chem Soc
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Chipot, C.1
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15
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0011639217
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Oxygen and nitrogen in competitive situations: Which is the hydrogen-bond acceptor?
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Böhm H-J, Brode S, Hesse U, Klebe G: Oxygen and nitrogen in competitive situations: which is the hydrogen-bond acceptor? Chem Eur J 1996, 2:1509-1513.
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Chem Eur J
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Böhm, H.-J.1
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16
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0042786508
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Development of an all-atom force field for heterocycles. Properties of liquid pyridine and diazenes
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in press
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Jorgensen WL, McDonald NA: Development of an all-atom force field for heterocycles. Properties of liquid pyridine and diazenes. J Mol Struct (Theochem) 1997, in press.
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(1997)
J Mol Struct (Theochem)
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Jorgensen, W.L.1
McDonald, N.A.2
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17
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0043189192
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Molecular recognition of carbohydrates: Interaction of diols with acetate ion
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Edited by Echegoyen L, Kaifer AE. The Netherlands: Kluwer Academic Publishers
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Jorgensen WL, Damm W, Frontera A, Lamb ML: Molecular recognition of carbohydrates: interaction of diols with acetate ion. In Physical Supramolecular Chemistry. Edited by Echegoyen L, Kaifer AE. The Netherlands: Kluwer Academic Publishers; 1996:115-126.
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Physical Supramolecular Chemistry
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Jorgensen, W.L.1
Damm, W.2
Frontera, A.3
Lamb, M.L.4
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18
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0000875754
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Computation of free energy changes in solution
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Edited by Schleyer PVR, Allinger NL, Clark T, Gasteiger J, Kollman PA, Schaefer HF. Chichester: John Wiley & Sons Ltd; in press
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Jorgensen WL: Computation of free energy changes in solution. In The Encyclopedia of Computational Chemistry. Edited by Schleyer PVR, Allinger NL, Clark T, Gasteiger J, Kollman PA, Schaefer HF. Chichester: John Wiley & Sons Ltd; 1997, in press.
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(1997)
The Encyclopedia of Computational Chemistry
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Jorgensen, W.L.1
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19
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0031058541
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The statistical-thermodynamic basis for computation of binding affinities
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Gilson MK, Given JA, Bush BL, McCammon JA: The statistical-thermodynamic basis for computation of binding affinities. Biophys J 1997, 72:1047-1069. This paper presents a detailed statistical-thermodynamic derivation and review of current methods for computing binding affinities. A modification to the double-annihilation method for computing binding affinities is proposed, and the ramifications of treating portions of a receptor as rigid are considered. The use of implicit (continuum) solvent models in free energy calculations is discussed, and a large section is devoted to entropic contributions to binding affinity.
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Biophys J
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Gilson, M.K.1
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20
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0002827429
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Computational insights on intermolecular interactions and binding in solution
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Jorgensen WL: Computational insights on intermolecular interactions and binding in solution. Chemtracts-Org Chem 1991, 4:91-119.
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Chemtracts-Org Chem
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Jorgensen, W.L.1
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0029731562
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Valence selectivity of the gramicidin channel: A molecular dynamics free energy perturbation study
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Roux B: Valence selectivity of the gramicidin channel: a molecular dynamics free energy perturbation study. Biophys J 1996, 71:3177-3185.
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Theoretical calculations of extraction selectivity: Alkali cation complexes of calix[4]-bis-crown6 in pure water, chloroform, and at a water/chloroform interface
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Varnek A, Wipff G: Theoretical calculations of extraction selectivity: alkali cation complexes of calix[4]-bis-crown6 in pure water, chloroform, and at a water/chloroform interface. J Comput Chem 1996, 17:1520-1531.
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J Comput Chem
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Computer simulations of the solvent dependence of apolar association strength: Gibbs free energy calculations on a cyclophanepyrene complex in water and chloroform
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Mordasini-Denti TZ, van Gunsteren WF, Diederich F: Computer simulations of the solvent dependence of apolar association strength: Gibbs free energy calculations on a cyclophanepyrene complex in water and chloroform. J Am Chem Soc 1996, 118:6044-6051.
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J Am Chem Soc
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0000954069
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4 not encapsulated by this host?
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4 not seen experimentally. Upon further analysis, the molecule was found to bind, bringing both calculated and experimental trends for the series into agreement.
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J Phys Chem
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Fox, T.1
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Synthesis and assembly of new molecular hosts: Solvation and the energetics of encapsulation
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Meissner R, Garcias X, Mecozzi S, Rebek J: Synthesis and assembly of new molecular hosts: solvation and the energetics of encapsulation. J Am Chem Soc 1997, 119:77-85.
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J Am Chem Soc
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Absolute configuration of bromochiorofluoromethane from molecular dynamics simulation of its enantioselective complexation by cryptophane-C
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Costante-Crassous J, Marrone TJ, Briggs JM, McCammon JA, Collet A: Absolute configuration of bromochiorofluoromethane from molecular dynamics simulation of its enantioselective complexation by cryptophane-C. J Am Chem Soc 1997, 119:3818-3823. FEP and TI calculations provided confirmation of the absolute configuration of CHFCIBr complexed by cryptophane C, in a manner independent of optical properties. The success with which both methods achieved the small target free energy difference must be in part due to the careful parameter optimization performed for the guest molecule, which included ab initio calculations and MC simulations of pure liquid CHFCIBr.
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J Am Chem Soc
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28
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0029844655
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Free energy perturbation studies on binding of A-74704 and its diester analog to HIV-1 protease
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2-symmetric inhibitor of HIV protease. Excellent results were obtained using multiple sampling protocols, and relatively inexpensive additional gas-phase calculations to obtain the ligand solvation free energy provide further validation for the approach used.
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Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions
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Åqvist J: Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions, J Comput Chem 1996, 17:1587-1597.
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Solvent effects in active-site molecular dynamics simulations on the binding of 8-methyl-N5-deazapterin and 8-methylpterin to dihydrofolate reductase
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Cummins PL, Gready JE: Solvent effects in active-site molecular dynamics simulations on the binding of 8-methyl-N5-deazapterin and 8-methylpterin to dihydrofolate reductase. J Comput Chem 1996, 17:1598-1611.
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Exploring the interaction between D-xylose isomerase and D-xylose by free energy calculation
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Approaches to protein-ligand binding from computer simulations
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Edited by Vergoten G, Theophanides T. The Netherlands: Kluwer Academic Publishers
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Jorgensen WL, Duffy EM, Essex JW, Severance DL, Blake JF, Jones-Hertzog DK, Lamb ML, Tirado-Rives J: Approaches to protein-ligand binding from computer simulations. In Biomolecular Structure and Dynamics: Recent Experimental and Theoretical Advances. Edited by Vergoten G, Theophanides T. The Netherlands: Kluwer Academic Publishers; 1997:21-34.
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Jorgensen, W.L.1
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35
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0030815020
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Computational binding studies of orthogonal cyclosporin-cyclophilin pairs
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Pierce AC, Jorgensen WL: Computational binding studies of orthogonal cyclosporin-cyclophilin pairs. Angew Chem Int Ed Engl 1997, 36:1466-1469. Control of protein-ligand recognition for gene therapy was investigated with a novel Monte Carlo-based free energy perturbation method. The observed binding differences for steric mutations in both protein and ligand over their wild type counterparts were reproduced.
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Angew Chem Int Ed Engl
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Pierce, A.C.1
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84961979250
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The structure and intermolecular interactions of a creatinine designed-receptor complex, studied by ab initio methods
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Craw JS, Cooper MD, Hillier IH: The structure and intermolecular interactions of a creatinine designed-receptor complex, studied by ab initio methods. J Chem Soc Perkin Trans 2 1997:869-871.
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J Chem Soc Perkin Trans 2
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0029905919
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Unexpected roles of guest polarizability and maximum hardness, and of host solvation in supramolecutar inclusion complexes: A dual theoretical and experimental study
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Castro R, Berardi MJ, Cordova E, de Olza MO, Kaifer AE, Evanseck JD: Unexpected roles of guest polarizability and maximum hardness, and of host solvation in supramolecutar inclusion complexes: a dual theoretical and experimental study. J Am Chem Soc 1996, 118:10257-10268.
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J Am Chem Soc
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Castro, R.1
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0029747145
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Gating as a control element in constrictive binding and guest release by hemicarcerands
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Houk KN, Nakamura K, Sheu C, Keating AE: Gating as a control element in constrictive binding and guest release by hemicarcerands. Science 1996, 273:627-629. Results of calculations of the conformational and energetic barriers to (de)complexation of guest molecules by hemicarcerands are summarized and support door and sliding door gating mechanisms that allow guest release from otherwise stable complexes.
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Science
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Houk, K.N.1
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0000750931
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Syntheses, binding properties, and structures of seven new hemicarcerands each composed of two bowls bridged by three tetramethylenedioxy groups and a fourth unique linkage
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Yoon J, Sheu CM, Houk KN, Knobler CB, Cram DJ: Syntheses, binding properties, and structures of seven new hemicarcerands each composed of two bowls bridged by three tetramethylenedioxy groups and a fourth unique linkage. J Org Chem 1996, 61:9323-9339.
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J Org Chem
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40
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Molecular mechanics and statistical thermodynamics studies of complexes of a flexible hemicarcerand with neutral guests
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Sheu C, Houk KN: Molecular mechanics and statistical thermodynamics studies of complexes of a flexible hemicarcerand with neutral guests. J Am Chem Soc 1996, 118:8056-8070.
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J Am Chem Soc
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Sheu, C.1
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0030989483
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Self-assembling ternary complex stabilities and template ratios in carceplex formation
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Nakamura K, Sheu C, Keating AE, Houk KN, Sherman JC, Chapman RG, Jorgensen WL: Self-assembling ternary complex stabilities and template ratios in carceplex formation. J Am Chem Soc 1997, 119:4321-4322.
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J Am Chem Soc
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Nakamura, K.1
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42
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0029955112
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Stabilization of a cis amide bond in a host-guest complex
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Pernia GJ, Kilburn JD, Essex JW, Mortishire-Smith RJ, Rowley M: Stabilization of a cis amide bond in a host-guest complex. J Am Chem Soc 1996, 118:10220-10227.
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J Am Chem Soc
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Self-assembly of [n]rotaxanes bearing dendritic stoppers
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Amabilino DB, Ashton PR, Balzani V, Brown CL, Credi A, Frechet JMJ, Leon JW, Raymo FM, Spencer N, Stoddart JF, Venturi M: Self-assembly of [n]rotaxanes bearing dendritic stoppers. J Am Chem Soc 1996, 118:12012-12020.
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J Am Chem Soc
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Jursic BS, Zdravkovski Z, French AD: Molecular modeling methodology of β-cyclodextrin inclusion complexes. J Mol Struct (Theochem) 1996, 366:113-117.
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