-
1
-
-
0034039797
-
Electrostatic aspects of protein-protein interactions
-
Sheinerman, F.B.; Norel, R.; Honig, B. Electrostatic aspects of protein-protein interactions. Curr. Opin. Struct. Biol., 2000, 10, 153-159.
-
(2000)
Curr. Opin. Struct. Biol
, vol.10
, pp. 153-159
-
-
Sheinerman, F.B.1
Norel, R.2
Honig, B.3
-
2
-
-
0034769223
-
Electrostatic contributions to protein-protein interactions: Fast energetic filters for docking and their physical basis
-
Norel, R.; Sheinerman, F.; Petrey, D.; Honig, B. Electrostatic contributions to protein-protein interactions: Fast energetic filters for docking and their physical basis. Protein Sci., 2001, 10, 2147-2161.
-
(2001)
Protein Sci
, vol.10
, pp. 2147-2161
-
-
Norel, R.1
Sheinerman, F.2
Petrey, D.3
Honig, B.4
-
3
-
-
0035160537
-
Barstar is electrostatically optimized for tight binding to barnase
-
Lee, L.P.; Tidor, B. Barstar is electrostatically optimized for tight binding to barnase. Nat. Struct. Biol., 2001, 8, 73-76.
-
(2001)
Nat. Struct. Biol
, vol.8
, pp. 73-76
-
-
Lee, L.P.1
Tidor, B.2
-
4
-
-
35348821202
-
Virtual screening strategies in drug discovery
-
McInnes, C. Virtual screening strategies in drug discovery. Curr. Opin. Chem. Biol., 2007, 11, 494-502.
-
(2007)
Curr. Opin. Chem. Biol
, vol.11
, pp. 494-502
-
-
McInnes, C.1
-
5
-
-
0002606755
-
Virtual screening-an overview
-
Walters, W.P.; Stahl, M.T.; Murcko, M.A. Virtual screening-an overview. Drug Discov. Today, 1998, 3, 160-178.
-
(1998)
Drug Discov. Today
, vol.3
, pp. 160-178
-
-
Walters, W.P.1
Stahl, M.T.2
Murcko, M.A.3
-
6
-
-
3042988525
-
Conformational analysis 130. MM2. A hydrocarbon force field utilizing V1 and V2 torsional terms
-
Allinger, N.L. Conformational analysis 130. MM2. A hydrocarbon force field utilizing V1 and V2 torsional terms. J. Am. Chem. Soc., 1977, 99, 8127-8134.
-
(1977)
J. Am. Chem. Soc
, vol.99
, pp. 8127-8134
-
-
Allinger, N.L.1
-
8
-
-
0024821263
-
Molecular Mechanics. The MM3 force field for hydrocarbons
-
Allinger, N.L.; Yuh, Y.H.; Lii, J.-H. Molecular Mechanics. The MM3 force field for hydrocarbons. J. Am. Chem. Soc., 1989, 111, 8551-8565.
-
(1989)
J. Am. Chem. Soc
, vol.111
, pp. 8551-8565
-
-
Allinger, N.L.1
Yuh, Y.H.2
Lii, J.-H.3
-
9
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minmimization, and dynamics calculations.
-
Brooks, B.R.; Bruccoleri, R.E.; Olafson, B.D.; States, D.J.; Swaminathan, S.; Karplus, M. CHARMM: A program for macromolecular energy, minmimization, and dynamics calculations. . J. Comput. Chem., 1983, 4, 187-217.
-
(1983)
J. Comput. Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
10
-
-
0024843595
-
-
Lii, J.-H.; Allinger, N.L. Molecular Mechanics. The MM3 force field for hydrocarbons. 2. vibrational frequencies and thermodynamics. J. Am. Chem. Soc., 1989, 111, 8566-8575.
-
Lii, J.-H.; Allinger, N.L. Molecular Mechanics. The MM3 force field for hydrocarbons. 2. vibrational frequencies and thermodynamics. J. Am. Chem. Soc., 1989, 111, 8566-8575.
-
-
-
-
11
-
-
0024804228
-
Molecular mechanics. The MM3 force field for hydrocarbons. 3. The van der Waals' potentials and crystal data for aliphatic and aromatic hydrocarbons
-
Lii, J.-H.; Allinger, N.L. Molecular mechanics. The MM3 force field for hydrocarbons. 3. The van der Waals' potentials and crystal data for aliphatic and aromatic hydrocarbons. J. Am. Chem. Soc., 1989, 111, 8576-8582.
-
(1989)
J. Am. Chem. Soc
, vol.111
, pp. 8576-8582
-
-
Lii, J.-H.1
Allinger, N.L.2
-
12
-
-
84986528070
-
The MM3 force field for amides, polypeptides and proteins
-
Lii, J.-H.; Allinger, N.L. The MM3 force field for amides, polypeptides and proteins. J. Comput. Chem., 1991, 12, 186-199.
-
(1991)
J. Comput. Chem
, vol.12
, pp. 186-199
-
-
Lii, J.-H.1
Allinger, N.L.2
-
13
-
-
84986518863
-
AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions
-
Weiner, P.K.; Kollman, P.A. AMBER: assisted model building with energy refinement. A general program for modeling molecules and their interactions. J. Comput. Chem., 1981, 2, 287-303.
-
(1981)
J. Comput. Chem
, vol.2
, pp. 287-303
-
-
Weiner, P.K.1
Kollman, P.A.2
-
14
-
-
0021757436
-
A new force field for molecular mechanical simulation of nucleic acids and proteins
-
Weiner, S.J.; Kollman, P.A.; Case, D.A.; Singh, U.C.; Ghio, C.; Alagona, G.; Profeta, S.J.; Weiner, P.K. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc., 1984, 106, 765-784.
-
(1984)
J. Am. Chem. Soc
, vol.106
, pp. 765-784
-
-
Weiner, S.J.1
Kollman, P.A.2
Case, D.A.3
Singh, U.C.4
Ghio, C.5
Alagona, G.6
Profeta, S.J.7
Weiner, P.K.8
-
15
-
-
84988053694
-
An all atom force field for simulations of proteins and nucleic acids
-
Weiner, S.J.; Kollman, P.A.; Nguyen, D.T.; Case, D.A. An all atom force field for simulations of proteins and nucleic acids. J. Comput. Chem., 1986, 7, 230-252.
-
(1986)
J. Comput. Chem
, vol.7
, pp. 230-252
-
-
Weiner, S.J.1
Kollman, P.A.2
Nguyen, D.T.3
Case, D.A.4
-
16
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen, W.L.; Maxwell, D.S.; 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.
-
(1996)
J. Am. Chem. Soc
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado Rives, J.3
-
17
-
-
0000795938
-
Freeenergies of hydration and pure liquid properties of hydrocarbons from the opls all-atom model
-
Kaminski, G.; Duffy, E.M.; Matsui, T.; Jorgensen, W.L. Freeenergies of hydration and pure liquid properties of hydrocarbons from the opls all-atom model. J. Phys. Chem., 1994, 98, 13077-13082.
-
(1994)
J. Phys. Chem
, vol.98
, pp. 13077-13082
-
-
Kaminski, G.1
Duffy, E.M.2
Matsui, T.3
Jorgensen, W.L.4
-
18
-
-
0041784950
-
-
MacKerell, A.D.; Bashford, D.; Bellott, M.; Dunbrack, R.L.; Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; 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. Phys. Chem. B, 1998, 102, 3586-3616.
-
MacKerell, A.D.; Bashford, D.; Bellott, M.; Dunbrack, R.L.; Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; 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. Phys. Chem. B, 1998, 102, 3586-3616.
-
-
-
-
19
-
-
0029011701
-
A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules
-
Cornell, W.D.; Cieplak, P.; Bayly, C.I.; Gould, I.R.; Merz, K.M.; Ferguson, D.M.; Spellmeyer, D.C.; Fox, T.; Caldwell, J.W.; Kollman, P.A. A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules. J. Am. Chem. Soc., 1995, 117, 5179.
-
(1995)
J. Am. Chem. Soc
, vol.117
, pp. 5179
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
20
-
-
0001242234
-
Characterization of MMFF94, MMFF94s, and other widely available force fields for conformational energies and for intermolecular-interaction energies and geometries
-
Halgren, T.A. MMFF VII. Characterization of MMFF94, MMFF94s, and other widely available force fields for conformational energies and for intermolecular-interaction energies and geometries. J. Comput. Chem., 1999, 20, 730-748.
-
(1999)
J. Comput. Chem
, vol.20
, pp. 730-748
-
-
Halgren VII, T.A.M.1
-
21
-
-
0008819754
-
The GROMOS biomolecular simulation program package
-
Scott, W.R.P.; Hunenberger, P.H.; Tironi, I.G.; Mark, A.E.; Billeter, S.R.; Fennen, J.; Torda, A.E.; Huber, T.; Kruger, P.; van Gunsteren, W.F. The GROMOS biomolecular simulation program package. J. Phys. Chem. A, 1999, 103, 3596-3607.
-
(1999)
J. Phys. Chem. A
, vol.103
, pp. 3596-3607
-
-
Scott, W.R.P.1
Hunenberger, P.H.2
Tironi, I.G.3
Mark, A.E.4
Billeter, S.R.5
Fennen, J.6
Torda, A.E.7
Huber, T.8
Kruger, P.9
van Gunsteren, W.F.10
-
23
-
-
33746597823
-
Fluctuating charge force fields: Recent developments and applications from small molecules to macromolecular biological systems
-
Patel, S.; Brooks, C.L. Fluctuating charge force fields: Recent developments and applications from small molecules to macromolecular biological systems. Mol. Simul., 2006, 32, 231-249.
-
(2006)
Mol. Simul
, vol.32
, pp. 231-249
-
-
Patel, S.1
Brooks, C.L.2
-
24
-
-
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., 2005, 26, 915-931.
-
(2005)
J. Comput. Chem
, vol.26
, pp. 915-931
-
-
Cho, A.E.1
Guallar, V.2
Berne, B.J.3
Friesner, R.4
-
25
-
-
33846212271
-
Comparison of shape-matching and docking as virtual screening tools
-
Hawkins, P.C.D.; Skillman, A.G.; Nicholls, A. Comparison of shape-matching and docking as virtual screening tools. J. Med. Chem., 2007, 50, 74-82.
-
(2007)
J. Med. Chem
, vol.50
, pp. 74-82
-
-
Hawkins, P.C.D.1
Skillman, A.G.2
Nicholls, A.3
-
26
-
-
34547673017
-
Comparison of topological, shape, and docking methods in virtual screening
-
McGaughey, G.B.; Sheridan, R.P.; Bayly, C.I.; Culberson, J.C.; Kreatsoulas, C.; Lindsley, S.; Maiorov, V.; Truchon, J.F.; Cornell, W.D. Comparison of topological, shape, and docking methods in virtual screening. J. Chem. Inf. Model., 2007, 47, 1504-1519.
-
(2007)
J. Chem. Inf. Model
, vol.47
, pp. 1504-1519
-
-
McGaughey, G.B.1
Sheridan, R.P.2
Bayly, C.I.3
Culberson, J.C.4
Kreatsoulas, C.5
Lindsley, S.6
Maiorov, V.7
Truchon, J.F.8
Cornell, W.D.9
-
27
-
-
33644862638
-
Scaffold hopping through virtual screening using 2D and 3D similarity descriptors: Ranking, voting, and consensus scoring
-
Zhang, Q.; Muegge, I. Scaffold hopping through virtual screening using 2D and 3D similarity descriptors: Ranking, voting, and consensus scoring. J. Med. Chem., 2006, 49, 1536-1548.
-
(2006)
J. Med. Chem
, vol.49
, pp. 1536-1548
-
-
Zhang, Q.1
Muegge, I.2
-
28
-
-
33646875701
-
Quantum mechanics in structure-based drug design
-
Peters, M.B.; Raha, K.; Merz, K.M. Quantum mechanics in structure-based drug design. Curr. Opin. Drug Discov. Dev., 2006, 9, 370-379.
-
(2006)
Curr. Opin. Drug Discov. Dev
, vol.9
, pp. 370-379
-
-
Peters, M.B.1
Raha, K.2
Merz, K.M.3
-
29
-
-
34548430376
-
The role of quantum mechanics in structure-based drug design
-
Raha, K.; Peters, M.B.; Wang, B.; Yu, N.; WollaCott, A.M.; Westerhoff, L.M.; Merz, K.M. The role of quantum mechanics in structure-based drug design. Drug Discov. Today, 2007, 12, 725-731.
-
(2007)
Drug Discov. Today
, vol.12
, pp. 725-731
-
-
Raha, K.1
Peters, M.B.2
Wang, B.3
Yu, N.4
WollaCott, A.M.5
Westerhoff, L.M.6
Merz, K.M.7
-
30
-
-
0017100947
-
Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
-
Warshel, A.; Levitt, M. Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol., 1976, 103, 227-249.
-
(1976)
J. Mol. Biol
, vol.103
, pp. 227-249
-
-
Warshel, A.1
Levitt, M.2
-
32
-
-
33746381417
-
Combining quantum mechanics methods with molecular mechanics methods in ONIOM
-
Vreven, T.; Byun, K.S.; Komaromi, I.; Dapprich, S.; Montgomery, J.A.; Morokuma, K.; Frisch, M.J. Combining quantum mechanics methods with molecular mechanics methods in ONIOM. J. Chem. Theor. Comput., 2006, 2, 815-826.
-
(2006)
J. Chem. Theor. Comput
, vol.2
, pp. 815-826
-
-
Vreven, T.1
Byun, K.S.2
Komaromi, I.3
Dapprich, S.4
Montgomery, J.A.5
Morokuma, K.6
Frisch, M.J.7
-
33
-
-
22244451417
-
Large-scale validation of a quantum mechanics based scoring function: Predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes
-
Raha, K.; Merz, K.M. Large-scale validation of a quantum mechanics based scoring function: Predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes. J. Med. Chem., 2005, 48, 4558-4575.
-
(2005)
J. Med. Chem
, vol.48
, pp. 4558-4575
-
-
Raha, K.1
Merz, K.M.2
-
34
-
-
84986527758
-
IMOMM-A new integrated ab-initio plus molecular mechanics geometry optimization scheme of equilibrium structures and transition-states
-
Maseras, M.; Morokuma, K. IMOMM-A new integrated ab-initio plus molecular mechanics geometry optimization scheme of equilibrium structures and transition-states. J. Comput. Chem., 1995, 16, 1170-1179.
-
(1995)
J. Comput. Chem
, vol.16
, pp. 1170-1179
-
-
Maseras, M.1
Morokuma, K.2
-
35
-
-
0041468782
-
On the application of the IMOMO (integrated molecular orbital plus molecular orbital) method
-
Vreven, T.; Morokuma, K. On the application of the IMOMO (integrated molecular orbital plus molecular orbital) method. J. Comput. Chem., 2000, 16, 1419-1432.
-
(2000)
J. Comput. Chem
, vol.16
, pp. 1419-1432
-
-
Vreven, T.1
Morokuma, K.2
-
36
-
-
31144441067
-
A multilayered integrated MO+MM method for geometry optimizations and single point energy predictions. A test for Diels-Alder reactions and Pt(P(t-Bu)(3)) (2)+H-2 oxidative addition
-
Svensson, M.; Humbel, S.; Froese, R.D.J.; Matsubara, T.; Sieber, S.; Morokuma, K. ONIOM: A multilayered integrated MO+MM method for geometry optimizations and single point energy predictions. A test for Diels-Alder reactions and Pt(P(t-Bu)(3)) (2)+H-2 oxidative addition. J. Phys. Chem., 1996, 100, 19357-19363.
-
(1996)
J. Phys. Chem
, vol.100
, pp. 19357-19363
-
-
Svensson, M.1
Humbel, S.2
Froese, R.D.J.3
Matsubara, T.4
Sieber, S.5
Morokuma6
ONIOM, K.7
-
37
-
-
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., 1999, 20, 1468-1494.
-
(1999)
J. Comput. Chem
, vol.20
, pp. 1468-1494
-
-
Philipp, D.M.1
Friesner, R.A.2
-
38
-
-
0000411659
-
A generalized hybrid orbital (GHO) method for the treatment of boundary atoms in combined QM/MM calculations
-
Gao, J.L.; Amara, P.; Alhambra, C.; Field, M.J. 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.
-
(1998)
J. Phys. Chem. A
, vol.102
, pp. 4714-4721
-
-
Gao, J.L.1
Amara, P.2
Alhambra, C.3
Field, M.J.4
-
39
-
-
42449130535
-
Hepatitis C virus NS5B polymerase: QM/MM calculations show the important role of the internal energy in ligand binding
-
Parks, J.M.; Kondru, R.K.; Hu, H.; Beratan, D.N.; Yang, W.T. Hepatitis C virus NS5B polymerase: QM/MM calculations show the important role of the internal energy in ligand binding. J. Phys. Chem. B, 2008, 112, 3168-3176.
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 3168-3176
-
-
Parks, J.M.1
Kondru, R.K.2
Hu, H.3
Beratan, D.N.4
Yang, W.T.5
-
40
-
-
23944459025
-
A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands
-
Khandelwal, A.; Lukacova, V.; Comez, D.; Kroll, D.M.; Raha, S.; Balaz, S. A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands. J. Med. Chem., 2005, 48, 5437-5447.
-
(2005)
J. Med. Chem
, vol.48
, pp. 5437-5447
-
-
Khandelwal, A.1
Lukacova, V.2
Comez, D.3
Kroll, D.M.4
Raha, S.5
Balaz, S.6
-
41
-
-
34548808607
-
QM/MM linear response method distinguishes ligand affinities for closely related metalloproteins
-
Khandelwal, A.; Balaz, S. QM/MM linear response method distinguishes ligand affinities for closely related metalloproteins. Proteins Struct. Funct. Genet., 2007, 69, 326-339.
-
(2007)
Proteins Struct. Funct. Genet
, vol.69
, pp. 326-339
-
-
Khandelwal, A.1
Balaz, S.2
-
42
-
-
34547688945
-
Relative binding affinities of fructose-1,6-bisphosphatase inhibitors calculated using a quantum mechanics-based free energy perturbation method
-
Reddy, M.R.; Erion, M.D. 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.
-
(2007)
J. Am. Chem. Soc
, vol.129
, pp. 9296-9297
-
-
Reddy, M.R.1
Erion, M.D.2
-
43
-
-
11144235131
-
A combined QM/MM approach to protein-ligand interactions: Polarization effects of the HIV-1 protease on selected high affinity inhibitors
-
Hensen, C.; Hermann, J.C.; Nam, K.H.; Ma, S.H.; Gao, J.L.; Holtje, H.D. A combined QM/MM approach to protein-ligand interactions: Polarization effects of the HIV-1 protease on selected high affinity inhibitors. J. Med. Chem., 2004, 47, 6673-6680.
-
(2004)
J. Med. Chem
, vol.47
, pp. 6673-6680
-
-
Hensen, C.1
Hermann, J.C.2
Nam, K.H.3
Ma, S.H.4
Gao, J.L.5
Holtje, H.D.6
-
44
-
-
57449089629
-
Assessing the role of polarization in docking
-
Illingworth, C.J.R.; Morris, G.M.; Parkes, K.E.B.; Snell, C.R.; Reynolds, C.A. Assessing the role of polarization in docking. J. Phys. Chem. A, 2008, 112, 12157-12163.
-
(2008)
J. Phys. Chem. A
, vol.112
, pp. 12157-12163
-
-
Illingworth, C.J.R.1
Morris, G.M.2
Parkes, K.E.B.3
Snell, C.R.4
Reynolds, C.A.5
-
45
-
-
77949358046
-
-
Qsite Schrodinger, LLC
-
Qsite Schrodinger, LLC.
-
-
-
-
46
-
-
77949407847
-
-
Glide Schrodinger, LLC
-
Glide Schrodinger, LLC.
-
-
-
-
47
-
-
38149017792
-
Binding free energy calculation for duocarmycin/DNA complex based on the QPLD-derived partial charge model
-
Zhong, H.; Kirschner, K.N.; Lee, M.; Bowen, J.P. Binding free energy calculation for duocarmycin/DNA complex based on the QPLD-derived partial charge model. Bioorg. Med. Chem. Lett. 2008, 18, 542-545.
-
(2008)
Bioorg. Med. Chem. Lett
, vol.18
, pp. 542-545
-
-
Zhong, H.1
Kirschner, K.N.2
Lee, M.3
Bowen, J.P.4
-
48
-
-
33644882236
-
-
Spiegel, K.; Rothlisberger, U.; Carloni, P. Duocarmycins Binding to DNA investigated by molecular simulations. 2006, 110, 3647-3660.
-
(2006)
Duocarmycins Binding to DNA investigated by molecular simulations
, vol.110
, pp. 3647-3660
-
-
Spiegel, K.1
Rothlisberger, U.2
Carloni, P.3
-
49
-
-
77949397261
-
Extension of QM/MM docking and its applications to metalloproteins
-
in press
-
Cho, A.E.; Rinaldo, D. Extension of QM/MM docking and its applications to metalloproteins. 2009, in press.
-
(2009)
-
-
Cho, A.E.1
Rinaldo, D.2
-
50
-
-
0027125907
-
A Priori evaluation of aqueous polarization effects through monte carlo QM-MM simulations
-
Gao, J.; Xia, X. A Priori evaluation of aqueous polarization effects through monte carlo QM-MM simulations. Science, 1992, 258, 631-635.
-
(1992)
Science
, vol.258
, pp. 631-635
-
-
Gao, J.1
Xia, X.2
-
51
-
-
0037459224
-
Importance of substrate and cofactor polarization in the active site of dehydrofolate reductase
-
Garcia-Viloca, M.; Truhlar, D.G.; Gao, J. Importance of substrate and cofactor polarization in the active site of dehydrofolate reductase. J. Mol. Biol., 2003, 327, 549-560.
-
(2003)
J. Mol. Biol
, vol.327
, pp. 549-560
-
-
Garcia-Viloca, M.1
Truhlar, D.G.2
Gao, J.3
-
52
-
-
0036882094
-
Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests
-
Kaminski, G.A.; Stern, H.A.; Berne, B.J.; Friesner, R.A.; Cao, Y.X.; Murphy, R.B.; Zhou, R.; Halgren, T.A. Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests. J. Comput. Chem., 2002, 23, 1515-1531.
-
(2002)
J. Comput. Chem
, vol.23
, pp. 1515-1531
-
-
Kaminski, G.A.1
Stern, H.A.2
Berne, B.J.3
Friesner, R.A.4
Cao, Y.X.5
Murphy, R.B.6
Zhou, R.7
Halgren, T.A.8
-
53
-
-
30444431852
-
A polarizable force field and continuum solvation methodology for modeling of protein-ligand interactions
-
Maple, J.R.; Cao, Y.; Damm, W.; Halgren, T.A.; Kaminski, G.A.; Zhang, L.Y.; Friesner, R.A. A polarizable force field and continuum solvation methodology for modeling of protein-ligand interactions. J. Chem. Theory Comput., 2005, 1, 694-715.
-
(2005)
J. Chem. Theory Comput
, vol.1
, pp. 694-715
-
-
Maple, J.R.1
Cao, Y.2
Damm, W.3
Halgren, T.A.4
Kaminski, G.A.5
Zhang, L.Y.6
Friesner, R.A.7
-
54
-
-
0242468112
-
Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF
-
Piquemal, J.P.; Williams-Hubbard, B.; Fey, N.; Deeth, R.J.; Gresh, N.; Giessner-Prettre, C. Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF. J. Comput. Chem., 2003, 24, 1963-1970.
-
(2003)
J. Comput. Chem
, vol.24
, pp. 1963-1970
-
-
Piquemal, J.P.1
Williams-Hubbard, B.2
Fey, N.3
Deeth, R.J.4
Gresh, N.5
Giessner-Prettre, C.6
-
55
-
-
0000560203
-
Fluctuating charge, polarizable dipole, and combined models: Parameterization from ab initio quantum chemistry
-
Stern, H.A.; Kaminski, G.A.; Banks, J.L.; Zhou, R.; Berne, B.J.; Friesner, R.A. Fluctuating charge, polarizable dipole, and combined models: Parameterization from ab initio quantum chemistry J. Phys. Chem. B, 1999, 103, 4730-4737.
-
(1999)
J. Phys. Chem. B
, vol.103
, pp. 4730-4737
-
-
Stern, H.A.1
Kaminski, G.A.2
Banks, J.L.3
Zhou, R.4
Berne, B.J.5
Friesner, R.A.6
-
56
-
-
0037260956
-
Development of a simple, self-consistent polarizable model for liquid water
-
Yu, H.; Hansson, T.; Gunsteren, W.F.v. Development of a simple, self-consistent polarizable model for liquid water. J. Chem. Phys., 2003, 118, 221-234.
-
(2003)
J. Chem. Phys
, vol.118
, pp. 221-234
-
-
Yu, H.1
Hansson, T.2
Gunsteren, W.F.V.3
-
57
-
-
0036890275
-
Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations
-
Ren, P.Y.; Ponder, J.W. Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. J. Comput. Chem., 2002, 23, 1497-1506.
-
(2002)
J. Comput. Chem
, vol.23
, pp. 1497-1506
-
-
Ren, P.Y.1
Ponder, J.W.2
-
58
-
-
0037899660
-
Polarizable atomic multipole water model for molecular mechanics simulation
-
Ren, P.; Ponder, J.W. Polarizable atomic multipole water model for molecular mechanics simulation J. Phys. Chem. B, 2003, 107, 5933-5947.
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 5933-5947
-
-
Ren, P.1
Ponder, J.W.2
-
59
-
-
36649021120
-
Design of a next generation force field: The X-POL potential
-
Xie, W.S.; Gao, J.L. Design of a next generation force field: The X-POL potential. J. Chem. Theor. Comput., 2007, 3, 1890-1900.
-
(2007)
J. Chem. Theor. Comput
, vol.3
, pp. 1890-1900
-
-
Xie, W.S.1
Gao, J.L.2
-
60
-
-
0030734211
-
Toward a molecular orbital derived empirical potential for liquid simulations
-
Gao, J.L. Toward a molecular orbital derived empirical potential for liquid simulations. J. Phys. Chem. B, 1997, 101, 657-663.
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 657-663
-
-
Gao, J.L.1
-
61
-
-
0001035485
-
A molecular-orbital derived polarization potential for liquid water
-
Gao, J.L. A molecular-orbital derived polarization potential for liquid water. J. Chem. Phys., 1998, 109, 2346-2354.
-
(1998)
J. Chem. Phys
, vol.109
, pp. 2346-2354
-
-
Gao, J.L.1
-
62
-
-
33645522435
-
A selfconsistent space-domain decomposition method for QM/MM computations of protein electrostatic potentials
-
Gascon, J.A.; Leung, S.S.F.; Batista, E.R.; Batista, V.S. A selfconsistent space-domain decomposition method for QM/MM computations of protein electrostatic potentials. J. Chem. Theor. Comput., 2006, 2, 175-186.
-
(2006)
J. Chem. Theor. Comput
, vol.2
, pp. 175-186
-
-
Gascon, J.A.1
Leung, S.S.F.2
Batista, E.R.3
Batista, V.S.4
-
63
-
-
43849107972
-
Optimization of cutting schemes for the evaluation of molecular electrostatic potentials in proteins via Moving-Domain QM/MM
-
Menikarachchi, L.; Gascón, J. Optimization of cutting schemes for the evaluation of molecular electrostatic potentials in proteins via Moving-Domain QM/MM. J. Mol. Model., 2008, 14, 479-487.
-
(2008)
J. Mol. Model
, vol.14
, pp. 479-487
-
-
Menikarachchi, L.1
Gascón, J.2
-
64
-
-
3042524904
-
A wellbehaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
-
Bayly, C.I.; Cieplak, P.; Cornell, W.; Kollman, P.A. A wellbehaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J. Phys. Chem., 1993, 97, 10269-10280.
-
(1993)
J. Phys. Chem
, vol.97
, pp. 10269-10280
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.3
Kollman, P.A.4
-
65
-
-
0031192137
-
-
Winn, P.J.; Ferenczy, G.G.; Reynolds, C.A. toward improved force fields. 1. multipole-derived atomic charges. 1997, 101, 5437-5445.
-
Winn, P.J.; Ferenczy, G.G.; Reynolds, C.A. toward improved force fields. 1. multipole-derived atomic charges. 1997, 101, 5437-5445.
-
-
-
-
66
-
-
0031188229
-
Toward improved force fields. 2. effective distributed multipoles
-
Ferenczy, G.G.; Winn, P.J.; Reynolds, C.A. Toward improved force fields. 2. effective distributed multipoles. 1997, 101, 5446-5455.
-
(1997)
, vol.101
, pp. 5446-5455
-
-
Ferenczy, G.G.1
Winn, P.J.2
Reynolds, C.A.3
-
67
-
-
33846426835
-
A computational study of the protein-ligand interactions in CDK2 inhibitors: Using quantum mechanics/molecular mechanics interaction energy as a predictor of the biological activity
-
Alzate-Morales, J.H.; Contreras, R.; Soriano, A.; Tunon, I.; Silla, E. A computational study of the protein-ligand interactions in CDK2 inhibitors: Using quantum mechanics/molecular mechanics interaction energy as a predictor of the biological activity. Biophys. J., 2007, 92, 430-439.
-
(2007)
Biophys. J
, vol.92
, pp. 430-439
-
-
Alzate-Morales, J.H.1
Contreras, R.2
Soriano, A.3
Tunon, I.4
Silla, E.5
-
68
-
-
34748912966
-
A quantum mechanics/molecular mechanics study of the protein-ligand interaction for inhibitors of HIV-1 integrase
-
Alves, C.N.; Marti, S.; Castillo, R.; Andres, J.; Moliner, V.; Tunon, I.; Silla, E. A quantum mechanics/molecular mechanics study of the protein-ligand interaction for inhibitors of HIV-1 integrase. Chem. Eur. J., 2007, 13, 7715-7724.
-
(2007)
Chem. Eur. J
, vol.13
, pp. 7715-7724
-
-
Alves, C.N.1
Marti, S.2
Castillo, R.3
Andres, J.4
Moliner, V.5
Tunon, I.6
Silla, E.7
-
69
-
-
41649100340
-
A quantum mechanic/molecular mechanic study of the wild-type and N155S mutant HIV-1 integrase complexed with diketo acid
-
Alves, C.N.; Marti, S.; Castillo, R.; Andres, J.; Moliner, V.; Tunon, I.; Silla, E. A quantum mechanic/molecular mechanic study of the wild-type and N155S mutant HIV-1 integrase complexed with diketo acid. Biophys. J., 2008, 94, 2443-2451.
-
(2008)
Biophys. J
, vol.94
, pp. 2443-2451
-
-
Alves, C.N.1
Marti, S.2
Castillo, R.3
Andres, J.4
Moliner, V.5
Tunon, I.6
Silla, E.7
-
70
-
-
1542377504
-
Quantum mechanical/molecular mechanical (QM/MM) docking: An evaluation for known test systems
-
Beierlein, F.; Lanig, H.; Schurer, G.; Horn, A.H.C.; Clark, T. Quantum mechanical/molecular mechanical (QM/MM) docking: an evaluation for known test systems. Mol. Phys., 2003, 101, 2469-2480.
-
(2003)
Mol. Phys
, vol.101
, pp. 2469-2480
-
-
Beierlein, F.1
Lanig, H.2
Schurer, G.3
Horn, A.H.C.4
Clark, T.5
-
71
-
-
42749088112
-
Prediction of the receptor conformation for iGluR2 agonist binding: QM/MM docking to an extensive conformational ensemble generated using normal mode analysis
-
Sander, T.; Lijefors, T.; Balle, T. Prediction of the receptor conformation for iGluR2 agonist binding: QM/MM docking to an extensive conformational ensemble generated using normal mode analysis. J. Mol. Graph., 2008, 26, 1259-1268.
-
(2008)
J. Mol. Graph
, vol.26
, pp. 1259-1268
-
-
Sander, T.1
Lijefors, T.2
Balle, T.3
-
72
-
-
47149089463
-
Role of structural water molecule in HIV proteaseinhibitor complexes: A QM/MM study
-
Suresh, C.H.; Vargheese, A.M.; Vijayalakshmi, K.P.; Mohan, N.; Koga, N. Role of structural water molecule in HIV proteaseinhibitor complexes: A QM/MM study. J. Comput. Chem., 2008, 29, 1840-1849.
-
(2008)
J. Comput. Chem
, vol.29
, pp. 1840-1849
-
-
Suresh, C.H.1
Vargheese, A.M.2
Vijayalakshmi, K.P.3
Mohan, N.4
Koga, N.5
-
73
-
-
36549018723
-
Hybrid quantum mechanical/molecular mechanical molecular dynamics simulations of HIV-1 integrase/inhibitor complexes
-
Nunthaboot, N.; Pianwanit, S.; Parasuk, V.; Ebalunode, J.O.; Briggs, J.M.; Kokpol, S. Hybrid quantum mechanical/molecular mechanical molecular dynamics simulations of HIV-1 integrase/inhibitor complexes. Biophys. J., 2007, 93, 3613-3626.
-
(2007)
Biophys. J
, vol.93
, pp. 3613-3626
-
-
Nunthaboot, N.1
Pianwanit, S.2
Parasuk, V.3
Ebalunode, J.O.4
Briggs, J.M.5
Kokpol, S.6
-
74
-
-
33845569858
-
A combined quantum mechanical and molecular mechanical study of the reaction mechanism and alphaamino acidity in alanine racemase
-
Major, D.T.; Gao, J.L. A combined quantum mechanical and molecular mechanical study of the reaction mechanism and alphaamino acidity in alanine racemase. J. Am. Chem. Soc., 2006, 128, 16345-16357.
-
(2006)
J. Am. Chem. Soc
, vol.128
, pp. 16345-16357
-
-
Major, D.T.1
Gao, J.L.2
-
75
-
-
33645699595
-
Molecular mechanisms of antibiotic resistance: QM/MM modelling of deacylation in a class A beta-lactamase
-
Hermann, J.C.; Ridder, L.; Hotje, H.D.; Mulholland, A.J. Molecular mechanisms of antibiotic resistance: QM/MM modelling of deacylation in a class A beta-lactamase. Org. Biomol. Chem., 2006, 4, 206-210.
-
(2006)
Org. Biomol. Chem
, vol.4
, pp. 206-210
-
-
Hermann, J.C.1
Ridder, L.2
Hotje, H.D.3
Mulholland, A.J.4
-
76
-
-
57449115580
-
Interpretation of protein/ligand crystal structure using QM/MM calculations: Case of HIV-1 protease/metallacarborane complex
-
Fanfrlik, J.; Brynda, J.; Rezac, J.; Hobza, P.; Lepsik, M. Interpretation of protein/ligand crystal structure using QM/MM calculations: case of HIV-1 protease/metallacarborane complex. J. Phys. Chem. B, 2008, 112, 15094-15102.
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 15094-15102
-
-
Fanfrlik, J.1
Brynda, J.2
Rezac, J.3
Hobza, P.4
Lepsik, M.5
|