-
1
-
-
77956166424
-
Docking to erlotinib off-targets leads to inhibitors of lung cancer cell proliferation with suitable in vitro pharmacokinetics
-
Li, L.; Li, J.; Khanna, M.; Jo, I.; Baird, J. P.; Meroueh, S. O. Docking to erlotinib off-targets leads to inhibitors of lung cancer cell proliferation with suitable in vitro pharmacokinetics ACS Med. Chem. Lett. 2010, 1, 229-233
-
(2010)
ACS Med. Chem. Lett.
, vol.1
, pp. 229-233
-
-
Li, L.1
Li, J.2
Khanna, M.3
Jo, I.4
Baird, J.P.5
Meroueh, S.O.6
-
2
-
-
84867370715
-
Efficient and accurate free energy calculations on trypsin inhibitors
-
De Ruiter, A.; Oostenbrink, C. Efficient and accurate free energy calculations on trypsin inhibitors J. Chem. Theory Comput. 2012, 8, 3686-3695
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 3686-3695
-
-
De Ruiter, A.1
Oostenbrink, C.2
-
3
-
-
22544456941
-
Peptide recognition by the T cell receptor: Comparison of binding free energies from thermodynamic integration, Poisson-Boltzmann and linear interaction energy approximations
-
Wan, S.; Coveney, P. V.; Flower, D. R. Peptide recognition by the T cell receptor: Comparison of binding free energies from thermodynamic integration, Poisson-Boltzmann and linear interaction energy approximations Philos. Trans. R. Soc., A 2005, 363, 2037-2053
-
(2005)
Philos. Trans. R. Soc., A
, vol.363
, pp. 2037-2053
-
-
Wan, S.1
Coveney, P.V.2
Flower, D.R.3
-
4
-
-
4544384195
-
The importance of a critical protonation state and the fate of the catalytic steps in class A β-lactamases and penicillin-binding proteins
-
Golemi-Kotra, D.; Meroueh, S. O.; Kim, C.; Vakulenko, S. B.; Bulychev, A.; Stemmler, A. J.; Stemmler, T. L.; Mobashery, S. The importance of a critical protonation state and the fate of the catalytic steps in class A β-lactamases and penicillin-binding proteins J. Biol. Chem. 2004, 279, 34665-34673
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 34665-34673
-
-
Golemi-Kotra, D.1
Meroueh, S.O.2
Kim, C.3
Vakulenko, S.B.4
Bulychev, A.5
Stemmler, A.J.6
Stemmler, T.L.7
Mobashery, S.8
-
5
-
-
0034736032
-
Simulations of the estrogen receptor ligand-binding domain: Affinity of natural ligands and xenoestrogens
-
Oostenbrink, C. B.; Pitera, J. W.; Van Lipzig, M. M. H.; Meerman, J. H. N.; Van Gunsteren, W. F. Simulations of the estrogen receptor ligand-binding domain: Affinity of natural ligands and xenoestrogens J. Med. Chem. 2000, 43, 4594-4605
-
(2000)
J. Med. Chem.
, vol.43
, pp. 4594-4605
-
-
Oostenbrink, C.B.1
Pitera, J.W.2
Van Lipzig, M.M.H.3
Meerman, J.H.N.4
Van Gunsteren, W.F.5
-
6
-
-
84863098112
-
Thermodynamic integration to predict host-guest binding affinities
-
Lawrenz, M.; Wereszczynski, J.; Ortiz-Sánchez, J.; Nichols, S.; McCammon, J. A. Thermodynamic integration to predict host-guest binding affinities J. Comput-Aided. Mol. Des. 2012, 26, 569-576
-
(2012)
J. Comput-Aided. Mol. Des.
, vol.26
, pp. 569-576
-
-
Lawrenz, M.1
Wereszczynski, J.2
Ortiz-Sánchez, J.3
Nichols, S.4
McCammon, J.A.5
-
7
-
-
84861188449
-
Free energy calculations on the binding of novel thiolactomycin derivatives to E. Coli fatty acid synthase i
-
Steinbrecher, T.; Case, D. A.; Labahn, A. Free energy calculations on the binding of novel thiolactomycin derivatives to E. coli fatty acid synthase I Bioorg. Med. Chem. 2012, 20, 3446-3453
-
(2012)
Bioorg. Med. Chem.
, vol.20
, pp. 3446-3453
-
-
Steinbrecher, T.1
Case, D.A.2
Labahn, A.3
-
8
-
-
77955813570
-
Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy
-
Lawrenz, M.; Wereszczynski, J.; Amaro, R.; Walker, R.; Roitberg, A.; McCammon, J. A. Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy Proteins: Struct., Funct., Bioinf. 2010, 78, 2523-2532
-
(2010)
Proteins: Struct., Funct., Bioinf.
, vol.78
, pp. 2523-2532
-
-
Lawrenz, M.1
Wereszczynski, J.2
Amaro, R.3
Walker, R.4
Roitberg, A.5
McCammon, J.A.6
-
9
-
-
84864199587
-
ZINC: A free tool to discover chemistry for biology
-
Irwin, J. J.; Sterling, T.; Mysinger, M. M.; Bolstad, E. S.; Coleman, R. G. ZINC: A free tool to discover chemistry for biology J. Chem. Inf. Model. 2012, 52, 1757-1768
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 1757-1768
-
-
Irwin, J.J.1
Sterling, T.2
Mysinger, M.M.3
Bolstad, E.S.4
Coleman, R.G.5
-
10
-
-
0031891022
-
Computation of electrostatic complements to proteins: A case of charge stabilized binding
-
Chong, L. T.; Dempster, S. E.; Hendsch, Z. S.; Lee, L.-P.; Tidor, B. Computation of electrostatic complements to proteins: A case of charge stabilized binding Protein Sci. 1998, 7, 206-210
-
(1998)
Protein Sci.
, vol.7
, pp. 206-210
-
-
Chong, L.T.1
Dempster, S.E.2
Hendsch, Z.S.3
Lee, L.-P.4
Tidor, B.5
-
11
-
-
0242443693
-
Force fields for protein simulations
-
Ponder, J. W.; Case, D. A. Force fields for protein simulations Adv. Protein Chem. 2003, 66, 27-85
-
(2003)
Adv. Protein Chem.
, vol.66
, pp. 27-85
-
-
Ponder, J.W.1
Case, D.A.2
-
12
-
-
0036771626
-
Accelerated Poisson-Boltzmann calculations for static and dynamic systems
-
Luo, R.; David, L.; Gilson, M. K. Accelerated Poisson-Boltzmann calculations for static and dynamic systems J. Comput. Chem. 2002, 23, 1244-1253
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 1244-1253
-
-
Luo, R.1
David, L.2
Gilson, M.K.3
-
13
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still, C. W.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. Semianalytical treatment of solvation for molecular mechanics and dynamics J. Am. Chem. Soc. 1990, 112, 6127-6129
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 6127-6129
-
-
Still, C.W.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
14
-
-
0000127140
-
Method for estimating the configurational entropy of macromolecules
-
Karplus, M.; Kushick, J. N. Method for estimating the configurational entropy of macromolecules Macromolecules 1981, 14, 325-332
-
(1981)
Macromolecules
, vol.14
, pp. 325-332
-
-
Karplus, M.1
Kushick, J.N.2
-
15
-
-
0034811498
-
Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA
-
Wang, J.; Morin, P.; Wang, W.; Kollman, P. A. Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA J. Am. Chem. Soc. 2001, 123, 5221-5230
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 5221-5230
-
-
Wang, J.1
Morin, P.2
Wang, W.3
Kollman, P.A.4
-
16
-
-
0034645763
-
Knowledge-based scoring function to predict protein-ligand interactions
-
Gohlke, H.; Hendlich, M.; Klebe, G. Knowledge-based scoring function to predict protein-ligand interactions J. Mol. Biol. 2000, 295, 337-356
-
(2000)
J. Mol. Biol.
, vol.295
, pp. 337-356
-
-
Gohlke, H.1
Hendlich, M.2
Klebe, G.3
-
17
-
-
33749511033
-
Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study
-
Basdevant, N.; Weinstein, H.; Ceruso, M. Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study J. Am. Chem. Soc. 2006, 128, 12766-12777
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 12766-12777
-
-
Basdevant, N.1
Weinstein, H.2
Ceruso, M.3
-
18
-
-
33645994825
-
Flexibility and conformational entropy in protein-protein binding
-
Grünberg, R.; Nilges, M.; Leckner, J. Flexibility and conformational entropy in protein-protein binding Structure 2006, 14, 683-693
-
(2006)
Structure
, vol.14
, pp. 683-693
-
-
Grünberg, R.1
Nilges, M.2
Leckner, J.3
-
19
-
-
80054904239
-
Solvent interaction energy calculations on molecular dynamics trajectories: Increasing the efficiency using systematic frame selection
-
Lill, M. A.; Thompson, J. J. Solvent interaction energy calculations on molecular dynamics trajectories: Increasing the efficiency using systematic frame selection J. Chem. Inf. Model. 2011, 51, 2680-2689
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 2680-2689
-
-
Lill, M.A.1
Thompson, J.J.2
-
20
-
-
43949128085
-
PDBcal: A comprehensive dataset for receptor-ligand interactions with three-dimensional structures and binding thermodynamics from isothermal titration calorimetry
-
Li, L.; Dantzer, J. J.; Nowacki, J.; O'Callaghan, B. J.; Meroueh, S. O. PDBcal: A comprehensive dataset for receptor-ligand interactions with three-dimensional structures and binding thermodynamics from isothermal titration calorimetry Chem. Biol. Drug Des. 2008, 71, 529-532
-
(2008)
Chem. Biol. Drug Des.
, vol.71
, pp. 529-532
-
-
Li, L.1
Dantzer, J.J.2
Nowacki, J.3
O'Callaghan, B.J.4
Meroueh, S.O.5
-
21
-
-
79955401050
-
Target-specific support vector machine scoring in structure-based virtual screening: Computational validation, in vitro testing in kinases, and effects on lung cancer cell proliferation
-
Li, L.; Khanna, M.; Jo, I.; Wang, F.; Ashpole, N. M.; Hudmon, A.; Meroueh, S. O. Target-specific support vector machine scoring in structure-based virtual screening: Computational validation, in vitro testing in kinases, and effects on lung cancer cell proliferation J. Chem. Inf. Model. 2011, 51, 755-759
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 755-759
-
-
Li, L.1
Khanna, M.2
Jo, I.3
Wang, F.4
Ashpole, N.M.5
Hudmon, A.6
Meroueh, S.O.7
-
22
-
-
80053313926
-
Support vector regression scoring of receptor-ligand complexes for rank-ordering and virtual screening of chemical libraries
-
Li, L.; Wang, B.; Meroueh, S. O. Support vector regression scoring of receptor-ligand complexes for rank-ordering and virtual screening of chemical libraries J. Chem. Inf. Model. 2011, 51, 2132-2138
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 2132-2138
-
-
Li, L.1
Wang, B.2
Meroueh, S.O.3
-
23
-
-
0033614004
-
Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
-
Word, J. M.; Lovell, S. C.; Richardson, J. S.; Richardson, D. C. Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation J. Mol. Biol. 1999, 285, 1735-1747
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 1735-1747
-
-
Word, J.M.1
Lovell, S.C.2
Richardson, J.S.3
Richardson, D.C.4
-
24
-
-
0036890178
-
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
-
Jakalian, A.; Jack, D. B.; Bayly, C. I. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation J. Comput. Chem. 2002, 23, 1623-1641
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 1623-1641
-
-
Jakalian, A.1
Jack, D.B.2
Bayly, C.I.3
-
25
-
-
34248394606
-
-
University of California: San Fransico.
-
Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Pearlman, D. A.; Crowley, M.; Walker, R. C.; Zhang, W.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossváry, I.; Wong, K. F.; Paesani, F.; Wu, X.; Brozell, S. R.; Tsui, V.; Schafmeister, H.; Ross, W. S.; Kollman, P. A. AMBER9; University of California: San Fransico, 2006.
-
(2006)
AMBER9
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Merz, K.M.8
Pearlman, D.A.9
Crowley, M.10
Walker, R.C.11
Zhang, W.12
Wang, B.13
Hayik, S.14
Roitberg, A.15
Seabra, G.16
Kolossváry, I.17
Wong, K.F.18
Paesani, F.19
Wu, X.20
Brozell, S.R.21
Tsui, V.22
Schafmeister, H.23
Ross, W.S.24
Kollman, P.A.25
more..
-
26
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 79, 926-935
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
27
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical Calculations
-
Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J.; Kollman, P. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical Calculations J. Comput. Chem. 2003, 24, 1999-2012
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.C.4
Xiong, G.5
Zhang, W.6
Yang, R.7
Cieplak, P.8
Luo, R.9
Lee, T.10
Caldwell, J.11
Wang, J.12
Kollman, P.13
-
28
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes J. Comput. Phys. 1977, 23, 327-341
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.-P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
29
-
-
0032560959
-
Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices
-
Srinivasan, J.; Cheatham, T. E.; Cieplak, P.; Kollman, P. A.; Case, D. A. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices J. Am. Chem. Soc. 1998, 120, 9401-9409
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 9401-9409
-
-
Srinivasan, J.1
Cheatham, T.E.2
Cieplak, P.3
Kollman, P.A.4
Case, D.A.5
-
30
-
-
0034084991
-
Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding
-
Massova, I.; Kollman, P. A. Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding Perspect. Drug Discovery Des. 2000, 18, 113-135
-
(2000)
Perspect. Drug Discovery Des.
, vol.18
, pp. 113-135
-
-
Massova, I.1
Kollman, P.A.2
-
31
-
-
0034789590
-
An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis
-
Wang, W.; Lim, W. A.; Jakalian, A.; Wang, J.; Wang, J.; Luo, R.; Bayly, C. I.; Kollman, P. A. An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis J. Am. Chem. Soc. 2001, 123, 3986-3994
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 3986-3994
-
-
Wang, W.1
Lim, W.A.2
Jakalian, A.3
Wang, J.4
Wang, J.5
Luo, R.6
Bayly, C.I.7
Kollman, P.A.8
-
32
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
Honig, B.; Nicholls, A. Classical electrostatics in biology and chemistry Science 1995, 268, 1144-1149
-
(1995)
Science
, vol.268
, pp. 1144-1149
-
-
Honig, B.1
Nicholls, A.2
-
33
-
-
32844457567
-
Accurate calculation of hydration free energies using macroscopic solvent models
-
Sitkoff, D.; Sharp, K. A.; Honig, B. Accurate calculation of hydration free energies using macroscopic solvent models J. Phys. Chem. 1994, 98, 1978-1988
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
34
-
-
0000538815
-
Analytical molecular surface calculation
-
Connolly, M. L. Analytical molecular surface calculation J. Appl. Crystallogr. 1983, 16, 548-558
-
(1983)
J. Appl. Crystallogr.
, vol.16
, pp. 548-558
-
-
Connolly, M.L.1
-
35
-
-
33749603363
-
How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis
-
Tan, C.; Yang, L.; Luo, R. How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis J. Phys. Chem. B 2006, 110, 18680-18687
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 18680-18687
-
-
Tan, C.1
Yang, L.2
Luo, R.3
-
36
-
-
1842479952
-
Exploring protein native states and large-scale conformational changes with a modified Generalized Born model
-
Onufriev, A.; Bashford, D.; Case, D. A. Exploring protein native states and large-scale conformational changes with a modified Generalized Born model Proteins: Struct., Funct., Bioinf. 2004, 55, 383-394
-
(2004)
Proteins: Struct., Funct., Bioinf.
, vol.55
, pp. 383-394
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
37
-
-
20644449471
-
Modification of the Generalized Born model suitable for macromolecules
-
Onufriev, A.; Bashford, D.; Case, D. A. Modification of the Generalized Born model suitable for macromolecules J. Phys. Chem. B 2000, 104, 3712-3720
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 3712-3720
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
38
-
-
59849095562
-
Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations
-
Liang, S.; Li, L.; Hsu, W.-L.; Pilcher, M. N.; Uversky, V.; Zhou, Y.; Dunker, K. A.; Meroueh, S. O. Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations Biochemistry 2008, 48, 399-414
-
(2008)
Biochemistry
, vol.48
, pp. 399-414
-
-
Liang, S.1
Li, L.2
Hsu, W.-L.3
Pilcher, M.N.4
Uversky, V.5
Zhou, Y.6
Dunker, K.A.7
Meroueh, S.O.8
-
39
-
-
41349106542
-
Recommendations for evaluation of computational methods
-
Jain, A.; Nicholls, A. Recommendations for evaluation of computational methods J. Comput.-Aided Mol. Des. 2008, 22, 133-139
-
(2008)
J. Comput.-Aided Mol. Des.
, vol.22
, pp. 133-139
-
-
Jain, A.1
Nicholls, A.2
-
40
-
-
75849162018
-
Incorporating receptor flexibility in the molecular design of protein interfaces
-
Li, L.; Liang, S.; Pilcher, M. M.; Meroueh, S. O. Incorporating receptor flexibility in the molecular design of protein interfaces Protein Eng., Des. Sel. 2009, 22, 575-586
-
(2009)
Protein Eng., Des. Sel.
, vol.22
, pp. 575-586
-
-
Li, L.1
Liang, S.2
Pilcher, M.M.3
Meroueh, S.O.4
-
41
-
-
0027991081
-
Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation
-
Lee, K. H.; Xie, D.; Freire, E.; Amzel, M. L. Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation Proteins: Struct., Funct., Bioinf. 1994, 20, 68-84
-
(1994)
Proteins: Struct., Funct., Bioinf.
, vol.20
, pp. 68-84
-
-
Lee, K.H.1
Xie, D.2
Freire, E.3
Amzel, M.L.4
|