-
1
-
-
0036606483
-
Principles of docking: An overview of search algorithms and a guide to scoring functions
-
Halperin, I., Ma, B.Y., Wolfson, H. & Nussinov, R. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins-Structure Function and Genetics 47, 409-443 (2002).
-
(2002)
Proteins-Structure Function and Genetics
, vol.47
, pp. 409-443
-
-
Halperin, I.1
Ma, B.Y.2
Wolfson, H.3
Nussinov, R.4
-
2
-
-
0030111106
-
Molecular docking towards drug discovery
-
Gschwend, D.A., Good, A.C. & Kuntz, I.D. Molecular docking towards drug discovery. J. Mol. Recognit. 9, 175-186 (1996).
-
(1996)
J. Mol. Recognit
, vol.9
, pp. 175-186
-
-
Gschwend, D.A.1
Good, A.C.2
Kuntz, I.D.3
-
3
-
-
0035416126
-
High-throughput docking for lead generation
-
Abagyan, R. & Totrov, M. High-throughput docking for lead generation. Curr. Opin. Chem. Biol. 5, 375-382 (2001).
-
(2001)
Curr. Opin. Chem. Biol
, vol.5
, pp. 375-382
-
-
Abagyan, R.1
Totrov, M.2
-
4
-
-
0026730489
-
Structure-based strategies for drug design and discovery
-
Kuntz, I.D. Structure-based strategies for drug design and discovery. Science 257, 1078-1082 (1992).
-
(1992)
Science
, vol.257
, pp. 1078-1082
-
-
Kuntz, I.D.1
-
5
-
-
0034677966
-
Drug discovery: A historical perspective
-
Drews, J. Drug discovery: A historical perspective. Science 287, 1960-1964 (2000).
-
(2000)
Science
, vol.287
, pp. 1960-1964
-
-
Drews, J.1
-
7
-
-
11144313018
-
The MPSim-Dock hierarchical docking algorithm: Application to the eight trypsin inhibitor cocrystals
-
Cho, A.E. et al. The MPSim-Dock hierarchical docking algorithm: application to the eight trypsin inhibitor cocrystals. J. Comput. Chem. 26, 48-71 (2005).
-
(2005)
J. Comput. Chem
, vol.26
, pp. 48-71
-
-
Cho, A.E.1
-
8
-
-
0033388757
-
Ligand docking and screening with FlexX. Med
-
Kramer, B., Metz, G., Rarey, M. & Lengauer, T. Ligand docking and screening with FlexX. Med. Chem. Res. 9, 463-478 (1999).
-
(1999)
Chem. Res
, vol.9
, pp. 463-478
-
-
Kramer, B.1
Metz, G.2
Rarey, M.3
Lengauer, T.4
-
9
-
-
0041919542
-
Improved protein-ligand docking using GOLD
-
Verdonk, M.L., Cole, J.C., Hartshorn, M.J., Murray, C.W. & Taylor, R.D. Improved protein-ligand docking using GOLD. Proteins-Structure Function and Genetics 52, 609-623 (2003).
-
(2003)
Proteins-Structure Function and Genetics
, vol.52
, pp. 609-623
-
-
Verdonk, M.L.1
Cole, J.C.2
Hartshorn, M.J.3
Murray, C.W.4
Taylor, R.D.5
-
10
-
-
20344403522
-
Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical (QM/ MM) approach
-
Cho, A.E., Guallar, V., Berne, B.J. & Friesner, R. Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical (QM/ MM) approach. J. Comput. Chem. 26, 915-931 (2005).
-
(2005)
J. Comput. Chem
, vol.26
, pp. 915-931
-
-
Cho, A.E.1
Guallar, V.2
Berne, B.J.3
Friesner, R.4
-
11
-
-
56649118415
-
Effect of quantum mechanical charges in binding sites of metalloproteins
-
Cho, A.E. Effect of quantum mechanical charges in binding sites of metalloproteins. BioChip J. 1, 70-75 (2007).
-
(2007)
BioChip J
, vol.1
, pp. 70-75
-
-
Cho, A.E.1
-
12
-
-
7744244599
-
Recent advances in zinc enzymology
-
Lipscomb, W.N. & Strater, N. Recent advances in zinc enzymology. Chem. Rev. 96, 2375-2433 (1996).
-
(1996)
Chem. Rev
, vol.96
, pp. 2375-2433
-
-
Lipscomb, W.N.1
Strater, N.2
-
13
-
-
0035811217
-
Models for protein-zinc ion binding sites. II. The catalytic sites
-
Deerfield, D.W., Carter, C.W. & Pedersen, L.G. Models for protein-zinc ion binding sites. II. The catalytic sites. Int. J. Quantum Chem. 83, 150-165 (2001).
-
(2001)
Int. J. Quantum Chem
, vol.83
, pp. 150-165
-
-
Deerfield, D.W.1
Carter, C.W.2
Pedersen, L.G.3
-
14
-
-
0033743281
-
Metal binding in proteins: The effect of the dielectric medium
-
Dudev, T. & Lim, C. Metal binding in proteins: The effect of the dielectric medium. J. Phys. Chem. B 104, 3692-3694 (2000).
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 3692-3694
-
-
Dudev, T.1
Lim, C.2
-
16
-
-
0041654899
-
Docking studies of matrix metalloproteinase inhibitors: Zinc parameter optimization to improve the binding free energy prediction
-
Hu, X. & Shelver, W.H. Docking studies of matrix metalloproteinase inhibitors: zinc parameter optimization to improve the binding free energy prediction. J. Mol. Graph. 22, 115-126 (2003).
-
(2003)
J. Mol. Graph
, vol.22
, pp. 115-126
-
-
Hu, X.1
Shelver, W.H.2
-
17
-
-
23944459025
-
A combination of docking, QM /MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands
-
Khandelwal, A. et al. A combination of docking, QM /MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands. J. Med. Chem. 48, 5437-5447 (2005).
-
(2005)
J. Med. Chem
, vol.48
, pp. 5437-5447
-
-
Khandelwal, A.1
-
18
-
-
13344275187
-
Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase
-
Strynadka, N.C.J. et al. Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. Nat. Struct. Mol. Biol. 3, 233-239 (1996).
-
(1996)
Nat. Struct. Mol. Biol
, vol.3
, pp. 233-239
-
-
Strynadka, N.C.J.1
-
19
-
-
12144289984
-
Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
-
Friesner, R.A. et al. Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 47, 1739-1749 (2004).
-
(2004)
J. Med. Chem
, vol.47
, pp. 1739-1749
-
-
Friesner, R.A.1
-
20
-
-
0031226772
-
Empirical scoring functions. 1. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
-
Eldridge, M.D., Murray, C.W., Auton, T.R., Paolini, G.V. & Mee, R.P. Empirical scoring functions. 1. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J. Comput.-Aided Mol. Des. 11, 425-445 (1997).
-
(1997)
J. Comput. Aided Mol. Des
, vol.11
, pp. 425-445
-
-
Eldridge, M.D.1
Murray, C.W.2
Auton, T.R.3
Paolini, G.V.4
Mee, R.P.5
-
21
-
-
20344403522
-
Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical(QM/MM) approach
-
Cho, A.E., Guallar, V., Berne, B.J. & Friesner, R. Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical(QM/MM) approach. J. Comput. Chem. 26, 915-31 (2005).
-
(2005)
J. Comput. Chem
, vol.26
, pp. 915-931
-
-
Cho, A.E.1
Guallar, V.2
Berne, B.J.3
Friesner, R.4
-
22
-
-
0011644592
-
Thoughts about density functional theory in 1998
-
Kohn, W. Thoughts about density functional theory in 1998. J. Comput. Chem. 20, 1-1 (1999).
-
(1999)
J. Comput. Chem
, vol.20
, pp. 1-1
-
-
Kohn, W.1
-
23
-
-
0001508425
-
6-31G* basis set for atoms K through Zn
-
Rassolov, V.A., Pople, J.A., Ratner, M.A. & Windus, T.L. 6-31G* basis set for atoms K through Zn. J. Chem. Phys. 109, 1223-1229 (1998).
-
(1998)
J. Chem. Phys
, vol.109
, pp. 1223-1229
-
-
Rassolov, V.A.1
Pople, J.A.2
Ratner, M.A.3
Windus, T.L.4
-
24
-
-
0035879976
-
6-31G*basis set for third-row atoms
-
Rassolov, V.A., Ratner, M.A., Pople, J.A., Redfern, P.C. & Curtiss, L.A. 6-31G*basis set for third-row atoms. J. Comput. Chem. 22, 976-984 (2001).
-
(2001)
J. Comput. Chem
, vol.22
, pp. 976-984
-
-
Rassolov, V.A.1
Ratner, M.A.2
Pople, J.A.3
Redfern, P.C.4
Curtiss, L.A.5
-
25
-
-
70349963254
-
Diffuse functions in the 6-31G basis set for atoms K through Zn
-
Tran, J.M., Rassolov, V.A., Ratner, M.A. & Pople, J.A. Diffuse functions in the 6-31G basis set for atoms K through Zn. J. Am. Chem. Soc. 217, U443-U443 (1999).
-
(1999)
J. Am. Chem. Soc
, vol.217
-
-
Tran, J.M.1
Rassolov, V.A.2
Ratner, M.A.3
Pople, J.A.4
-
26
-
-
34250817103
-
A new mixing of hartree-fock and local density-functional theories
-
Becke, A.D. A new mixing of hartree-fock and local density-functional theories. J. Chem. Phys. 98, 1372-1377 (1993).
-
(1993)
J. Chem. Phys
, vol.98
, pp. 1372-1377
-
-
Becke, A.D.1
-
27
-
-
33645716728
-
Comparison of density-functional and Mp2 calculations on the water monomer and dimer
-
Kim, K. & Jordan, K.D. Comparison of density-functional and Mp2 calculations on the water monomer and dimer. J. Phys. Chem. A 98, 10089-10094 (1994).
-
(1994)
J. Phys. Chem. A
, vol.98
, pp. 10089-10094
-
-
Kim, K.1
Jordan, K.D.2
-
28
-
-
0001322105
-
Rationale for mixing exact exchange with density functional approximations
-
Perdew, J.P., Emzerhof, M. & Burke, K. Rationale for mixing exact exchange with density functional approximations. J. Chem. Phys. 105, 9982-9985 (1996).
-
(1996)
J. Chem. Phys
, vol.105
, pp. 9982-9985
-
-
Perdew, J.P.1
Emzerhof, M.2
Burke, K.3
-
29
-
-
33751157732
-
Ab-initio calculation of vibrational absorption and circular-dichroism spectra using density-functional force-fields
-
Stephens, P.J., Devlin, F.J., Chabalowski, C.F. & Frisch, M.J. Ab-initio calculation of vibrational absorption and circular-dichroism spectra using density- functional force-fields. J. Phys. Chem. A 98, 11623-11627 (1994).
-
(1994)
J. Phys. Chem. A
, vol.98
, pp. 11623-11627
-
-
Stephens, P.J.1
Devlin, F.J.2
Chabalowski, C.F.3
Frisch, M.J.4
-
30
-
-
0001420061
-
Mixed ab initio QM/ MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide
-
Philipp, D.M. & Friesner, R.A. Mixed ab initio QM/ MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide. J. Comput. Chem. 20, 1468-1494 (1999).
-
(1999)
J. Comput. Chem
, vol.20
, pp. 1468-1494
-
-
Philipp, D.M.1
Friesner, R.A.2
|