Chemistry Reference
In-Depth Information
[368] Homans SW. Water, water everywhere-except where it matters?, Drug Discov. Today,
2007, 12:534-539.
[369] Paesani F, 371Voth GA. The properties of water: insights from quantum simulations. J.
Phys. Chem. B, 2009,113: 5702-5719.
[370] Chong, SH, Ham S. Interaction with the Surrounding Water Plays a Key Role in
Determining the Aggregation Propensity of Proteins. Angewandte Chemie, International,
2014, 53:3961-3964.
[371] Valérie Vallet1, Jean-Pierre Flament1 and Michel Masella2, Revisiting a many-body model
for water based on a single polarizable site: From gas phase clusters to liquid and air/liquid
water systems, J. Chem. Phys. 2013, 139: 114502.
[372] Kirchmair J, Spitzer GM, Liedl KR. Considerationof water and solvation effects in virtual
screening. In virtual screening principles, challenges and practical guidelines, Scriffer CA,
Ed. Wiley-VCH Verlag: 2011, pp 263-289.
[373] Barillari C, Taylor J, Viner R Essex JW, Classification of water molecules in protein
binding sites. J. Am. Chem. Soc. 2007, 129: 2577-2587.
[374] Zahou T, Huang D, Caflish A. Quantum mechanical methods for drug design. Curr. Top.
Med. Chem. 2010, 10:33-45.
[375] Spiegela K, Magistrato A. Modeling anticancer drug-DNA interactions
via
mexed QM/MM
molecular dynamics simulations. Org. Biomol. Chem. 2006, 4: 2507-2517.
[376] Senn HM, Thiel W. QM/MM methods for biomolecular systems Angew. Chem. Int. Ed.
2009, 48:1198-1229.
[377] Menikarachchi LC, Gascon JA, QM/MM approaches in medicinal chemistry research.
Curr. Top. Med. Chem. 2010, 10: 46-54.
[378] Glao J, Amara P, Alhambra C, Field MJ. A generalized hybrid orbital (GHO) method for
the treatment of boundary atoms in combined QM/MM calculations. J. Phys. Chem. A.
1998, 102:4714-4721.
[379] Friesner RA. Combined quantum and molecular mechanics (QM/MM). Drug Disc. Today,
2004, 1: 253-260.
[380] Alzate-Morales JH, Contreras R, Soriano A, Tunon I, Silla E. A computational study of the
protein-ligand interaction in CDK2 inhibitors: using quantum mechanics/molecular
mechanics interaction energy as a predictor of the biological activity. Biophys. J. 2007, 92:
430-439.
[381] Willett P. Similarity-based virtual screening using 2D fingerprints. Drug Discovery Today,
2006, 11: 1046-1053.
[382] Satry M, Lowne JF, Dixon SL, Sherman W. Large-scale systematic analysis of 2D
fingerprint methods and parameters to improve virtual screening enrichments. J. Chem. Inf.
Model. 2010, 50: 771-784.
[383] Duan JX, Dixon SL, Lowrie JF, Sherman W. Analysis and comparison of 2D fingerprints:
Insights into database screening performance using eight fingerprint methods. J. Mol.
Graphics. Model. 2010, 20: 157-170.
[384] Schuffenhauer A, Gillet VJ, Willen P. Similarity searching in files of three-dimensional
chemical structure analysis of the BIOSTER database using two-dimensional fingerprints
and molecular field descriptors. J. Chem. Inf. Comput. Sci. 2000, 40: 295-307.
[385] Cheeseright TJ, Mackey MD, Melville JL, Vinter JG. FieldScreen: virtual screening using
molecular fields: Application to the DUD data set J. Chem. Inf. Model. 2008, 48: 2108-
2117.
[386] Kearsley SK, Smith GM. An alternative method for the alignment of molecular structures:
Maximizing electrostatic and steric overlap. Tetrahedron Comput.Meth. 1990, 3: 615-653.
