-
1
-
-
0025737742
-
Design of enzyme inhibitors using iterative protein crystallographic analysis
-
Appelt, K., Bacquet, R.J., Bartlett, C.A. et al. 1991. Design of enzyme inhibitors using iterative protein crystallographic analysis. J. Med. Chem. 34: 1925-1934.
-
(1991)
J. Med. Chem.
, vol.34
, pp. 1925-1934
-
-
Appelt, K.1
Bacquet, R.J.2
Bartlett, C.A.3
-
2
-
-
0026349524
-
Application of crystallographic and modeling methods in the design of purine nucleoside phosphorylase inhibitors
-
Ealick, S.E., Babu, Y.S., Bugg, C.E. et al. 1991. Application of crystallographic and modeling methods in the design of purine nucleoside phosphorylase inhibitors. Proc. Natl. Acad. Sci. USA 88: 11540-11544.
-
(1991)
Proc. Natl. Acad. Sci. USA
, vol.88
, pp. 11540-11544
-
-
Ealick, S.E.1
Babu, Y.S.2
Bugg, C.E.3
-
3
-
-
0028057975
-
Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors
-
Lam, P.Y., Jadhav, P.K., Eyermann, C.J. et al. 1994. Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors. Science 263: 380-384.
-
(1994)
Science
, vol.263
, pp. 380-384
-
-
Lam, P.Y.1
Jadhav, P.K.2
Eyermann, C.J.3
-
4
-
-
0027403420
-
Design of thymidylate synthase inhibitors using protein crystal structures: The synthesis and biological evaluation of a novel class of 5-substituted quinazolinones
-
Webber, S.E., Bleckman, T.M., Attard, J., Deal, J.D. et al. 1993. Design of thymidylate synthase inhibitors using protein crystal structures: the synthesis and biological evaluation of a novel class of 5-substituted quinazolinones. J. Med. Chem. 36: 733-746.
-
(1993)
J. Med. Chem.
, vol.36
, pp. 733-746
-
-
Webber, S.E.1
Bleckman, T.M.2
Attard, J.3
Deal, J.D.4
-
5
-
-
0023106632
-
Calculation of the relative change in binding free energy of a protein-inhibitor complex
-
Bash, P.A., Singh, U.C., Brown, F.K., Langridge, R., Kollman, P.A. 1987. Calculation of the relative change in binding free energy of a protein-inhibitor complex. Science 235: 574-576.
-
(1987)
Science
, vol.235
, pp. 574-576
-
-
Bash, P.A.1
Singh, U.C.2
Brown, F.K.3
Langridge, R.4
Kollman, P.A.5
-
6
-
-
0024578173
-
Free-energy via molecular simulation: Applications to chemical and biomolecular systems
-
Beveridge, D.L., Dicapua, F.M. 1989. Free-energy via molecular simulation: applications to chemical and biomolecular systems. Annu. Rev. Biophys. Bio. 18: 431-492.
-
(1989)
Annu. Rev. Biophys. Bio.
, vol.18
, pp. 431-492
-
-
Beveridge, D.L.1
Dicapua, F.M.2
-
7
-
-
0017100947
-
Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
-
Warshel, A., Levitt, M. 1976. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol. 103: 227-249.
-
(1976)
J. Mol. Biol.
, vol.103
, pp. 227-249
-
-
Warshel, A.1
Levitt, M.2
-
8
-
-
84988053595
-
-exchange reaction and gas phase protonation of polyethers
-
-exchange reaction and gas phase protonation of polyethers. J. Comput. Chem. 7: 718-730.
-
(1986)
J. Comput. Chem.
, vol.7
, pp. 718-730
-
-
Singh, U.C.1
Kollman, P.A.2
-
9
-
-
84986513644
-
A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
-
Field, M.J., Bash, P.A., Karplus, M. 1990. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J. Comput. Chem. 11: 700-733.
-
(1990)
J. Comput. Chem.
, vol.11
, pp. 700-733
-
-
Field, M.J.1
Bash, P.A.2
Karplus, M.3
-
10
-
-
84986527758
-
IMOMM: A new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states
-
Maseras, F., Morokuma, K. 1995. IMOMM: a new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states. J. Comput. Chem. 16: 1170-1179.
-
(1995)
J. Comput. Chem.
, vol.16
, pp. 1170-1179
-
-
Maseras, F.1
Morokuma, K.2
-
11
-
-
28644442414
-
Binding energy analysis for wild-type and Y181C mutant HIV-1 RT/8-Cl TIBO complex structures: Quantum chemical calculations based on the ONIOM method
-
Saen-oon, S., Kuno, M., Hannongbua, S. 2005. Binding energy analysis for wild-type and Y181C mutant HIV-1 RT/8-Cl TIBO complex structures: quantum chemical calculations based on the ONIOM method. Proteins 61: 859-869.
-
(2005)
Proteins
, vol.61
, pp. 859-869
-
-
Saen-oon, S.1
Kuno, M.2
Hannongbua, S.3
-
12
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
Honig, B., Nicholls, A. 1995. Classical electrostatics in biology and chemistry. Science 268: 1144-1149.
-
(1995)
Science
, vol.268
, pp. 1144-1149
-
-
Honig, B.1
Nicholls, A.2
-
13
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still, W.C., Tempczyk, A., Hawley, R.C., Hendrickson, T. 1990. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 112: 6127-6129.
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
14
-
-
84946893847
-
Electrostatic interaction of a solute with a continuum. A direct utilization of ab initio molecular potentials for the prevision of solvent effects
-
Miertius, S., Scrocco, E., Tomasi, J. 1981. Electrostatic interaction of a solute with a continuum. A direct utilization of ab initio molecular potentials for the prevision of solvent effects. Chem. Phys. 55: 117-129.
-
(1981)
Chem. Phys.
, vol.55
, pp. 117-129
-
-
Miertius, S.1
Scrocco, E.2
Tomasi, J.3
-
15
-
-
0032560959
-
Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices
-
Srinivasan, J., Cheatham, T.E. III, Cieplak, P., Kollman, P.A., Case, D.A. 1998. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J. Am. Chem. Soc. 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
-
16
-
-
0001019593
-
Design, synthesis, and kinetic evaluation of high-affinity FKBP ligands and the x-ray crystal structures of their complexes with FKBP12
-
Holt, D.A., Luengo, J.I., Yamashita, D.S. et al. 1993. Design, synthesis, and kinetic evaluation of high-affinity FKBP ligands and the x-ray crystal structures of their complexes with FKBP12. J. Am. Chem. Soc. 115: 9925-9938.
-
(1993)
J. Am. Chem. Soc.
, vol.115
, pp. 9925-9938
-
-
Holt, D.A.1
Luengo, J.I.2
Yamashita, D.S.3
-
17
-
-
0027325247
-
FK-506-binding protein: Three-dimensional structure of the complex with the antagonist L-685, 818
-
Becker, J.W., Rotonda, J., McKeever, B.M. et al. 1993. FK-506-binding protein: three-dimensional structure of the complex with the antagonist L-685, 818. J. Biol. Chem. 268: 11335-11339.
-
(1993)
J. Biol. Chem.
, vol.268
, pp. 11335-11339
-
-
Becker, J.W.1
Rotonda, J.2
McKeever, B.M.3
-
18
-
-
0030055657
-
Exploring the energy landscapes of molecular recognition by a genetic algorithm: Analysis of the requirements for robust docking of HIV-1 protease and FKBP-12 complexes
-
Verkhivker, M.G., Rejto, A.P., Gehlhaar, K.D., Freer, T.S. 1996. Exploring the energy landscapes of molecular recognition by a genetic algorithm: analysis of the requirements for robust docking of HIV-1 protease and FKBP-12 complexes. Proteins 25: 342-353.
-
(1996)
Proteins
, vol.25
, pp. 342-353
-
-
Verkhivker, M.G.1
Rejto, A.P.2
Gehlhaar, K.D.3
Freer, T.S.4
-
19
-
-
0031008974
-
Mean field analysis of FKBP12 complexes with FK506 and rapamycin: Implications for a role of crystallographic water molecules in molecular recognition and specificity
-
Rejto, A.P., Verkhivker, M.G. 1997. Mean field analysis of FKBP12 complexes with FK506 and rapamycin: implications for a role of crystallographic water molecules in molecular recognition and specificity. Proteins 28: 313-324.
-
(1997)
Proteins
, vol.28
, pp. 313-324
-
-
Rejto, A.P.1
Verkhivker, M.G.2
-
20
-
-
0033614989
-
32-Indolyl ether derivatives of ascomycin: Three-dimensional structures of complexes with FK506-binding protein
-
Becker, J.W., Retonda, J., Cryan, J.G. et al. 1999. 32-Indolyl ether derivatives of ascomycin: three-dimensional structures of complexes with FK506-binding protein. J. Med. Chem. 42: 2798-2804.
-
(1999)
J. Med. Chem.
, vol.42
, pp. 2798-2804
-
-
Becker, J.W.1
Retonda, J.2
Cryan, J.G.3
-
21
-
-
18044403602
-
2-Aryl-2, 2-difluoroacetamde FKBP12 ligands: Synthesis and X-ray structutal studies
-
Dubowchik, G.M., Vrudhula, V.M., Dasgupta, B. et al. 2001. 2-Aryl-2, 2-difluoroacetamde FKBP12 ligands: synthesis and X-ray structutal studies. Org. Lett. 3: 3987-3990.
-
(2001)
Org. Lett.
, vol.3
, pp. 3987-3990
-
-
Dubowchik, G.M.1
Vrudhula, V.M.2
Dasgupta, B.3
-
22
-
-
1542316339
-
Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: Binding of FK506 to FKBP
-
Zacharias, M. 2004. Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: binding of FK506 to FKBP. Proteins 54: 759-767.
-
(2004)
Proteins
, vol.54
, pp. 759-767
-
-
Zacharias, M.1
-
23
-
-
0025826967
-
Atomic structure of FKBP-FK506, an immunophilin-immunosuppressant complex
-
Duyne, G.D.V., Standaert, R.F., Karplus, P.A., Schreiber, S.L., Clardy, J. 1991. Atomic structure of FKBP-FK506, an immunophilin-immunosuppressant complex. Science 252: 839-842.
-
(1991)
Science
, vol.252
, pp. 839-842
-
-
Duyne, G.D.V.1
Standaert, R.F.2
Karplus, P.A.3
Schreiber, S.L.4
Clardy, J.5
-
24
-
-
0025955186
-
Atomic structure of the rapamycin human immunophilin FKBP12 complex
-
Duyne, G.D.V., Standaert, R.F., Schreiber, S.L., Clardy, J. 1991. Atomic structure of the rapamycin human immunophilin FKBP12 complex. J. Am. Chem. Soc. 113: 7433-7434.
-
(1991)
J. Am. Chem. Soc.
, vol.113
, pp. 7433-7434
-
-
Duyne, G.D.V.1
Standaert, R.F.2
Schreiber, S.L.3
Clardy, J.4
-
25
-
-
84893169025
-
General atomic and molecular electronic structure system
-
Schmidt, M.W., Baldridge, K.K., Boatz, J.A. et al. 1993. General atomic and molecular electronic structure system. J. Comput. Chem. 14: 1347-1363.
-
(1993)
J. Comput. Chem.
, vol.14
, pp. 1347-1363
-
-
Schmidt, M.W.1
Baldridge, K.K.2
Boatz, J.A.3
-
26
-
-
18344379477
-
-
St. Louis, MO: Tripos, Inc
-
SYBYL Version 6.9.1. 2003. St. Louis, MO: Tripos, Inc.
-
(2003)
SYBYL Version 6.9.1
-
-
-
27
-
-
0025398721
-
WHAT IF: A molecular modeling and drug design program
-
Vriend, G. 1990. WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8: 52-56.
-
(1990)
J. Mol. Graph.
, vol.8
, pp. 52-56
-
-
Vriend, G.1
-
28
-
-
34548243709
-
Extending the power of quantum chemistry to large systems with the fragment molecular orbital method
-
Fedorov, D.G., Kitaura, K. 2007. Extending the power of quantum chemistry to large systems with the fragment molecular orbital method. J. Phys. Chem. A 111: 6904-6914.
-
(2007)
J. Phys. Chem. A
, vol.111
, pp. 6904-6914
-
-
Fedorov, D.G.1
Kitaura, K.2
-
29
-
-
2342622178
-
The importance of three-body terms in the fragment molecular orbital method
-
Fedorov, D.G., Kitaura, K. 2004. The importance of three-body terms in the fragment molecular orbital method. J. Chem. Phys. 120: 6832-6840.
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 6832-6840
-
-
Fedorov, D.G.1
Kitaura, K.2
-
30
-
-
34249884543
-
Molecular recognition mechanism of FK506 binding protein: An all-electron fragment molecular orbital study
-
Nakanishi, I., Fedorov, D.G., Kitaura, K. 2007. Molecular recognition mechanism of FK506 binding protein: an all-electron fragment molecular orbital study. Proteins 68: 145-158.
-
(2007)
Proteins
, vol.68
, pp. 145-158
-
-
Nakanishi, I.1
Fedorov, D.G.2
Kitaura, K.3
-
31
-
-
11144282711
-
Ab initio quantum mechanical study of the binding energies of human estrogen receptor a with its ligands: An application of fragment molecular orbital method
-
Fukuzawa, K., Kitaura, K., Uebayasi, M. et al. 2005. Ab initio quantum mechanical study of the binding energies of human estrogen receptor a with its ligands: an application of fragment molecular orbital method. J. Comput. Chem. 26: 1-10.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1-10
-
-
Fukuzawa, K.1
Kitaura, K.2
Uebayasi, M.3
-
32
-
-
33846595219
-
Pair interaction energy decomposition analysis
-
Fedorov, D.G., Kitaura, K. 2007. Pair interaction energy decomposition analysis. J. Comput. Chem. 28: 222-237.
-
(2007)
J. Comput. Chem.
, vol.28
, pp. 222-237
-
-
Fedorov, D.G.1
Kitaura, K.2
-
33
-
-
0027125907
-
A priori evaluation of aqueous polarization effect through Monte Carlo QM-MM simulations
-
Gao, J., Xia, X. 1992. A priori evaluation of aqueous polarization effect through Monte Carlo QM-MM simulations. Science 258: 631-635.
-
(1992)
Science
, vol.258
, pp. 631-635
-
-
Gao, J.1
Xia, X.2
-
34
-
-
0037459224
-
Importance of substrate and cofactor polarization in the active site of dihydrofolate reductase
-
Garcia-Viloca, M., Truhlar, D.G., Gao, J. 2003. Importance of substrate and cofactor polarization in the active site of dihydrofolate reductase. J. Mol. Biol. 327: 549-560.
-
(2003)
J. Mol. Biol.
, vol.327
, pp. 549-560
-
-
Garcia-Viloca, M.1
Truhlar, D.G.2
Gao, J.3
-
35
-
-
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., Ma, S., Gao, J., Holtje, H.-D. 2004. A combined QM/MM approach to protein-ligand interactions: polarization effects of the HIV-1 protease on selected high affinity inhibitors. J. Med. Chem. 47: 6673-6680.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 6673-6680
-
-
Hensen, C.1
Hermann, J.C.2
Nam, K.3
Ma, S.4
Gao, J.5
Holtje, H.-D.6
-
36
-
-
20344362412
-
Protein/ligand binding free energies calculated with quantum mechanics/molecular mechanics
-
Gräter, F., Schwarzl, S.M., Dejaegere, A., Fischer, S., Smith, J.C. 2005. Protein/ligand binding free energies calculated with quantum mechanics/molecular mechanics. J. Phys. Chem. B 109: 10474-10483.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 10474-10483
-
-
Gräter, F.1
Schwarzl, S.M.2
Dejaegere, A.3
Fischer, S.4
Smith, J.C.5
-
37
-
-
0035910029
-
Computational study of protein specificity: The molecular basis of HIV-1 protease drug resistance
-
Wang, W., Kollman, P.A. 2001. Computational study of protein specificity: the molecular basis of HIV-1 protease drug resistance. Pro. Natl. Acad. Sci. USA 98: 14937-14942.
-
(2001)
Pro. Natl. Acad. Sci. USA
, vol.98
, pp. 14937-14942
-
-
Wang, W.1
Kollman, P.A.2
-
38
-
-
85135301704
-
-
San Diego, CA: Accelrys Software Inc
-
Discover and InsightII. 2005. San Diego, CA: Accelrys Software Inc.
-
(2005)
Discover and InsightII
-
-
-
39
-
-
0035913537
-
Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions
-
Rocchia, W., Alexov, E., Honig, B. 2001. Extending the applicability of the nonlinear Poisson-Boltzmann equation: multiple dielectric constants and multivalent ions. J. Phys. Chem. B 105: 6507-6514.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 6507-6514
-
-
Rocchia, W.1
Alexov, E.2
Honig, B.3
-
40
-
-
0037080244
-
Rapid grid-based construction of the molecular surface for both molecules and geometric objects: Applications to the finite difference Poisson-Boltzmann method
-
Rocchia, W., Sridharan, S., Nicholls, A. et al. 2002. Rapid grid-based construction of the molecular surface for both molecules and geometric objects: applications to the finite difference Poisson-Boltzmann method. J. Comput. Chem. 23: 128-137.
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 128-137
-
-
Rocchia, W.1
Sridharan, S.2
Nicholls, A.3
|