Chemistry Reference
In-Depth Information
[451] Ghersi D and Sanchez R. EasyMIFs and SiteHOUND: a tookit for the identification of ligand-binding sites in protein
structures. Structural bioinformatics. 2009;23:3185-3186.
[452] Mullins E, Liu YA, Ghaderi A and Fast SD. Sigma Profile Database for predicting solid solubility in pure and mixed
solvent mixtures for organic pharmacological compounds with cosmo-based thermodynamic methods. Ind. Eng. Chem.
Res 2008;47:1707-1725.
[453] Sun XM, Wei XG, Wu CXP, Ren Y, Wong NB and Li WK. Cooperative effect of solvent in the neutral hydration of
ketenimine:An ab initio study using the hybrid cluster/continuum model. J. Phys. Chem. A 2010;114:595-602.
[454] Shivakumar D, Deng Y and Roux B. Computations of absolute solvation free energies of small molecules using explicit
and implicit solvent model. J. of Chem. Theory and Computation. 2009;5:919-930.
[455] Reddy MR, Singh UC, Erion MD. LJ.Ab initio quantum mechanics-bsed free energy perturbation method for calculating
relative salvation free energies. Comput. Chem. 2007; 28:491-494.
[456] Reddy MR and Erion MD. Relative binding affinities of fructose-1.6-bisphosphatase inhibitors calculated using a quantum
mechanics-based free energy perturbation method. J. Am. Chem. Soc. 2007;129:9296-9297.
[457] Deng Y and Roux B. Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo
simulations. The Journal of Chemical Physics. 2008;128:115103-115111.
[458] Lerner MG, Meagher KL and Carlson HA. Automatied clustering of probe molecules from solvent mapping of protein
surfaces: new algorithms applied to hot-spot mapping and structure-based drug design. J. Comput. Aided Mol. Des.
2008;22:727-736.
[459] Hodak M, Chisnell R, Lu W and Bernholc J. Functional implications of multistage copper binding to the prion protein.
PNAS 2009;106:11756-11581.
[460] Shen J, Quiocho FA. Calculation of binding energy differences for receptor-ligand systems using the Poisson-Boltzmann
method. J. Comp. Chem. 1995;16:445-453.
[461] Kollman PA, Massova I, Reyes C, Kuhn B, Huso OS, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini AO, Cieplack,
Srinivasan P, Case J, Cheatham TE. Calculating structures and free energies of complex molecules:combining molecular
mechanics and continuum models. Acc. Chem. Res. 2000; 33:889-897.
[462] Tounge BA, Reynolds CH. Calculation of the binding affinity of β-secretase inhibitors using the linear interaction energy
method. J. Med. Chem. 2003;46:2074-2082.
[463] Cavalli A, Carloni P and Recanatini M. Tartet-related applications of first principles Quantum Chemical Methods in Drug
Design. Chemical Reviews. 2006;106:3497-3519.
[464] 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.
[465] Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox TG, Caldwell JW, Kollman
PA. A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc.
1996;117:5179-5197.
[466] MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, Field MJ, Fisher S, Gao J, Guo H, Ha S,
Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick, S, Ngo T, Nguyen DT, Prodhorn B, Reiher
WE III, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M.
All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phs. Chem. B. 1998;102:3586-
3616.
[467] Warshel A. Computer simulations of enzyme catalysis: Methods, progress and insights. Annu. Rev. Biophys. Biomol.
Struct. 2003;32:425-443.
[468] Car R, Parinello M. Unified approach for molecular dynamics and density-functional theory. Phys. Rev. Lett.
1985;55:2471-2474.
[469] Waller MP, Robertazzi A, Plats JA, Hibbs DE, Williams PA. Hybrid densitgy functional theory for π-stacking
interactions:Application to benzenes, pyridines and DNA bases. J. Comput. Chem. 2006;27:491-504.[470]
Hohenberg P, Kohn W. Inhomogeneous electron gas. Physical Review B 1964;136:864-871.; Kohn W, Sham L. Self-
consistent equations including exchange and correlation effects. J. Phys. Rev. A 1965;149:1133-1138.
[471] Dans PD and Coitiño, Density functional theory characterization and descriptive analysis of cisplatin and related
compounds. J. Chem. Inf. Model. 2009;49:1407-149.
[472] Guadarrama P, Soto-Castro D and Otero JR. Performance of DFT hybrid functional in the theoretical treatment of H-
bonds:Analysis term-by-term. International Journal of Quantum Chemistry 2007;108:229-237.
[473] Koch W, Holthausen MC. A Chemist's Guide to density functional theory: Wiley-VCH; Weinheim, Germany 2000.
[474] Parr RG, Yang W. Density functional theory of the electronic structure of molecules. Annu. Rev. Phys. Chem.
1995;46:701-728.
[475] Parr RG, Yang W. Density-functional theory of atoms and molecules. Oxford University Press: Oxford, UD, 1989.
