-
2
-
-
0013808622
-
Mechanism of action of penicillins: A proposal based on their structural similarity to acyl-D-alanyl-D-alanine
-
Tipper, D. J., and Strominger, J. L. (1965) Mechanism of action of penicillins: A proposal based on their structural similarity to acyl-D-alanyl-D-alanine, Proc. Natl. Acad. Sci. U.S.A. 54, 1133-1141.
-
(1965)
Proc. Natl. Acad. Sci. U.S.A.
, vol.54
, pp. 1133-1141
-
-
Tipper, D.J.1
Strominger, J.L.2
-
3
-
-
0001930562
-
-
Page, M. I., Ed. Blackie Academic & Professional, London
-
Frère, J. M., Nguyen-Distèche, M., Coyette, J., and Joris, B. (1992) in The Chemistry of Beta-Lactams (Page, M. I., Ed.) pp 148-197, Blackie Academic & Professional, London.
-
(1992)
The Chemistry of Beta-Lactams
, pp. 148-197
-
-
Frère, J.M.1
Nguyen-Distèche, M.2
Coyette, J.3
Joris, B.4
-
4
-
-
0029019031
-
Beta-lactamases and bacterial resistance to antibiotics
-
Frère, J. M. (1995) Beta-lactamases and bacterial resistance to antibiotics, Mol. Microbiol. 16, 385-395.
-
(1995)
Mol. Microbiol.
, vol.16
, pp. 385-395
-
-
Frère, J.M.1
-
5
-
-
0025270942
-
Beta-lactamases as fully efficient enzymes
-
Christensen, H., Martin, M. T., and Waley, S. G. (1990) Beta-lactamases as fully efficient enzymes, Biochem. J. 266, 853-861.
-
(1990)
Biochem. J.
, vol.266
, pp. 853-861
-
-
Christensen, H.1
Martin, M.T.2
Waley, S.G.3
-
6
-
-
0001817705
-
-
Page, M. I., Ed. Blackie Academic & Professional, London
-
Waley, S. G. (1992) in The Chemistry of Beta-Lactams (Page, M. I., Ed.) pp 199-227, Blackie Academic & Professional, London.
-
(1992)
The Chemistry of Beta-Lactams
, pp. 199-227
-
-
Waley, S.G.1
-
7
-
-
0031973490
-
Kinship and diversification of bacterial penicillin-binding proteins and beta-lactamases
-
Massova, I., and Mobashery, S. (1998) Kinship and diversification of bacterial penicillin-binding proteins and beta-lactamases, Antimicrob. Agents Chemother. 1-17.
-
(1998)
Antimicrob. Agents Chemother.
, pp. 1-17
-
-
Massova, I.1
Mobashery, S.2
-
8
-
-
0031898283
-
X-ray studies of enzymes that interact with penicillins
-
Kelly, J. A., Kuzin, A. P., Charlier, P., and Fonzé, E. (1998) X-ray studies of enzymes that interact with penicillins, Cell. Mol. Life Sci. 54, 353-358.
-
(1998)
Cell. Mol. Life Sci.
, vol.54
, pp. 353-358
-
-
Kelly, J.A.1
Kuzin, A.P.2
Charlier, P.3
Fonzé, E.4
-
9
-
-
0032032930
-
Catalytic properties of class A beta-lactamases: Eficiency and diversity
-
Matagne, A., Lamotte-Brasseur, J., and Frère, J. M. (1998) Catalytic properties of class A beta-lactamases: Eficiency and diversity, Biochem. J. 330, 581-598.
-
(1998)
Biochem. J.
, vol.330
, pp. 581-598
-
-
Matagne, A.1
Lamotte-Brasseur, J.2
Frère, J.M.3
-
10
-
-
0037460169
-
Insights into the acylation mechanism of class A beta-lactamases from molecular dynamics simulations of the TEM-1 enzyme complexed with benzylpenicillin
-
Díaz, N., Sordo, T. L., Merz, K. M., Jr., and Suárez, D. (2003) Insights into the acylation mechanism of class A beta-lactamases from molecular dynamics simulations of the TEM-1 enzyme complexed with benzylpenicillin, J. Am. Chem. Soc. 125, 672-684.
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 672-684
-
-
Díaz, N.1
Sordo, T.L.2
Merz Jr., K.M.3
Suárez, D.4
-
11
-
-
0037094114
-
An ultrahigh-resolution structure of TEM-1 beta-lactamase suggests a role for Glu166 as the general base in acylation
-
Minasov, G., Wang, X., and Shoichet, B. (2002) An ultrahigh-resolution structure of TEM-1 beta-lactamase suggests a role for Glu166 as the general base in acylation, J. Am. Chem. Soc. 124, 5333-5340.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 5333-5340
-
-
Minasov, G.1
Wang, X.2
Shoichet, B.3
-
12
-
-
0026801518
-
Molecular structure of the acyl-enzyme intermediate in β-lactam hydrolysis at 1.7 Å resolution
-
Strynadka, N. C. J., Adachi, H., Jensen, S. E., Johns, K., Sielecki, A., Betzel, C., Sutoh, K., and James, M. N. G. (1992) Molecular structure of the acyl-enzyme intermediate in β-lactam hydrolysis at 1.7 Å resolution, Nature 359, 700-705.
-
(1992)
Nature
, vol.359
, pp. 700-705
-
-
Strynadka, N.C.J.1
Adachi, H.2
Jensen, S.E.3
Johns, K.4
Sielecki, A.5
Betzel, C.6
Sutoh, K.7
James, M.N.G.8
-
13
-
-
0029738864
-
Crystal structure of 6α-(hydroxymethyl)penicillanate complexed to the TEM-1 β-lactamase from Escherichia coli: Evidence on the mechanism of action of a novel inhibitor designed by a computer-aided process
-
Maveyraud, L., Massova, I., Birck, C., Miyashita, K., Samama, J. P., and Mobashery, S. (1996) Crystal structure of 6α-(hydroxymethyl)penicillanate complexed to the TEM-1 β-lactamase from Escherichia coli: Evidence on the mechanism of action of a novel inhibitor designed by a computer-aided process, J. Am. Chem. Soc. 118, 7435-7440.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 7435-7440
-
-
Maveyraud, L.1
Massova, I.2
Birck, C.3
Miyashita, K.4
Samama, J.P.5
Mobashery, S.6
-
14
-
-
0035957080
-
Structures of the acyl-enzyme complexes of the Staphylococcus aureus beta-lactamase mutant Glu166Asp:Asn170Gln with benzylpenicillin and cephaloridine
-
Chen, C. C. H., and Herzberg, O. (2001) Structures of the acyl-enzyme complexes of the Staphylococcus aureus beta-lactamase mutant Glu166Asp:Asn170Gln with benzylpenicillin and cephaloridine, Biochemistry 40, 2351-2358.
-
(2001)
Biochemistry
, vol.40
, pp. 2351-2358
-
-
Chen, C.C.H.1
Herzberg, O.2
-
15
-
-
0031041590
-
Site-directed mutagenesis of glutamate 166 in two beta-lactamases
-
Guillaume, G., Vanhove, M., Lamotte-Brasseur, J., Ledent, P., Jamin, M., Joris, B., and Frère, J. M. (1997) Site-directed mutagenesis of glutamate 166 in two beta-lactamases, J. Biol. Chem. 272, 5438-5444.
-
(1997)
J. Biol. Chem.
, vol.272
, pp. 5438-5444
-
-
Guillaume, G.1
Vanhove, M.2
Lamotte-Brasseur, J.3
Ledent, P.4
Jamin, M.5
Joris, B.6
Frère, J.M.7
-
16
-
-
0025022490
-
Refined crystal structure of beta-lactamase from Citrobacter freundii indicates a mechanism for beta-lactam hydrolysis
-
Oefner, C., D'Arcy, D., Daly, J. J., Gubernator, K., Charnas, R. L., Heinze, I., Hubschwerlen, C., and Winkler, F. K. (1990) Refined crystal structure of beta-lactamase from Citrobacter freundii indicates a mechanism for beta-lactam hydrolysis. Nature 343, 284-288.
-
(1990)
Nature
, vol.343
, pp. 284-288
-
-
Oefner, C.1
D'Arcy, D.2
Daly, J.J.3
Gubernator, K.4
Charnas, R.L.5
Heinze, I.6
Hubschwerlen, C.7
Winkler, F.K.8
-
17
-
-
0027978868
-
The role of tyrosine 150 in catalysis of beta-lactam hydrolysis by AmpC beta-lactamase from Escherichia coli investigated by site-directed mutagenesis
-
Dubus, A., Normark, S., Kania, M., and Page, M. G. (1994) The role of tyrosine 150 in catalysis of beta-lactam hydrolysis by AmpC beta-lactamase from Escherichia coli investigated by site-directed mutagenesis, Biochemistry 33, 8577-8586.
-
(1994)
Biochemistry
, vol.33
, pp. 8577-8586
-
-
Dubus, A.1
Normark, S.2
Kania, M.3
Page, M.G.4
-
19
-
-
0035852621
-
A 1.2 Å snapshot of the final step of bacterial cell wall biosynthesis
-
Lee, W., McDonough, M. A., Kotra, L. P., Li, Z.-H., Silvaggi, N. R., Takeda, Y., Kelly, J. A., and Mobashery, S. (2001) A 1.2 Å snapshot of the final step of bacterial cell wall biosynthesis, Proc. Natl. Acad. Sci. U.S.A. 98, 1427-1431.
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 1427-1431
-
-
Lee, W.1
McDonough, M.A.2
Kotra, L.P.3
Li, Z.-H.4
Silvaggi, N.R.5
Takeda, Y.6
Kelly, J.A.7
Mobashery, S.8
-
20
-
-
0037432016
-
The crystal structure of phosphonate-inhibited D-Ala-D-Ala peptidase reveals an analogue of a tetrahedral transition state
-
Silvaggi, N. R., Anderson, J. W., Brinsmade, S. R., Pratt, R. F., and Kelly, J. A. (2003) The crystal structure of phosphonate-inhibited D-Ala-D-Ala peptidase reveals an analogue of a tetrahedral transition state, Biochemistry 42, 1199-1208.
-
(2003)
Biochemistry
, vol.42
, pp. 1199-1208
-
-
Silvaggi, N.R.1
Anderson, J.W.2
Brinsmade, S.R.3
Pratt, R.F.4
Kelly, J.A.5
-
21
-
-
2942682663
-
Mixed quantum mechanical/molecular mechanical study of the deacylation reaction in a penicillin binding protein versus in a class C beta-lactamase
-
Gherman, B. F., Goldberg, S. D., Cornish, V. W., and Friesner, R. A. (2004) Mixed quantum mechanical/molecular mechanical study of the deacylation reaction in a penicillin binding protein versus in a class C beta-lactamase, J. Am. Chem. Soc. 126, 7652-7654.
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 7652-7654
-
-
Gherman, B.F.1
Goldberg, S.D.2
Cornish, V.W.3
Friesner, R.A.4
-
22
-
-
0035807996
-
Critical involvement of a carbamylated lysine in the catalytic function of class D beta-lactamases
-
Golemi, D., Maveyraud, L., Vakulenko, S., Samama, J. P., and Mobashery, S. (2001) Critical involvement of a carbamylated lysine in the catalytic function of class D beta-lactamases, Proc. Natl. Acad. Sci. U.S.A. 98, 14280-14285.
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 14280-14285
-
-
Golemi, D.1
Maveyraud, L.2
Vakulenko, S.3
Samama, J.P.4
Mobashery, S.5
-
23
-
-
0035808477
-
Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 2.3 Å resolution
-
Davies, C., White, S. W., and Nicholas, R. A. (2001) Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 2.3 Å resolution, J. Biol. Chem. 276, 616-623.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 616-623
-
-
Davies, C.1
White, S.W.2
Nicholas, R.A.3
-
24
-
-
0035951090
-
Kinetic and mechanistic studies of penicillin-binding protein 2x from Streptococcus pneumoniae
-
Thomas, B., Wang, Y., and Stein, R. L. (2001) Kinetic and mechanistic studies of penicillin-binding protein 2x from Streptococcus pneumoniae, Biochemistry 40, 15811-15823.
-
(2001)
Biochemistry
, vol.40
, pp. 15811-15823
-
-
Thomas, B.1
Wang, Y.2
Stein, R.L.3
-
25
-
-
0347296368
-
Catalytic mechanism of the Streptomyces K15 DD-transpeptidase/penicillin- binding protein probed by site-directed mutagenesis and structural analysis
-
Rhazi, N., Charlier, P., Dehareng, D., Engher, D., Vermeire, M., Frère, J.-M., Nguyen-Distèche, M., and Fonzé, E. (2003) Catalytic mechanism of the Streptomyces K15 DD-transpeptidase/penicillin-binding protein probed by site-directed mutagenesis and structural analysis, Biochemistry 42, 2895-2906.
-
(2003)
Biochemistry
, vol.42
, pp. 2895-2906
-
-
Rhazi, N.1
Charlier, P.2
Dehareng, D.3
Engher, D.4
Vermeire, M.5
Frère, J.-M.6
Nguyen-Distèche, M.7
Fonzé, E.8
-
26
-
-
0022481365
-
Streptomyces K15 DD-peptidase-catalysed reactions with suicide beta-lactam carbonyl donors
-
Leyh-Bouille, M., Nguyen-Distèche, M., Pirlot, S., Vaithen, A., Bourguignon, C., and Ghuysen, J.-M. (1986) Streptomyces K15 DD-peptidase- catalysed reactions with suicide beta-lactam carbonyl donors, Biochem. J. 235, 177-182.
-
(1986)
Biochem. J.
, vol.235
, pp. 177-182
-
-
Leyh-Bouille, M.1
Nguyen-Distèche, M.2
Pirlot, S.3
Vaithen, A.4
Bourguignon, C.5
Ghuysen, J.-M.6
-
27
-
-
0033618429
-
The crystal structure of a penicilloyl-serine transferase of intermediate penicillin sensitivity
-
Fonzé, E., Vermeire, M., Nguyen-Distèche, M., Brasseur, R., and Charlier, P. (1999) The crystal structure of a penicilloyl-serine transferase of intermediate penicillin sensitivity, J. Biol. Chem. 274, 21853-21860.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 21853-21860
-
-
Fonzé, E.1
Vermeire, M.2
Nguyen-Distèche, M.3
Brasseur, R.4
Charlier, P.5
-
28
-
-
0042320537
-
Understanding the acylation mechanisms of active-site serine penicillin-recognizing proteins: A molecular dynamics simulation study
-
Oliva, M., Dideberg, O., and Field, M. J. (2003) Understanding the acylation mechanisms of active-site serine penicillin-recognizing proteins: A molecular dynamics simulation study, Proteins: Struct. Funct. Genet. 52, 88-100.
-
(2003)
Proteins: Struct. Funct. Genet.
, vol.52
, pp. 88-100
-
-
Oliva, M.1
Dideberg, O.2
Field, M.J.3
-
29
-
-
0004016501
-
Comparison of simple potential functions for the simulation of liquid water
-
Jorgensen, W. L., Chandrasekhar, J., Madura, J., Impey, R. W., and Klein, M. L. (1983) Comparison of simple potential functions for the simulation of liquid water, J. Chem. Phys. 79, 926-935.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.3
Impey, R.W.4
Klein, M.L.5
-
30
-
-
0004223683
-
-
University of California, San Francisco
-
Schafmeister, C., Ross, W. S., and Romanovski, V. (1995) LEaP, University of California, San Francisco.
-
(1995)
LEaP
-
-
Schafmeister, C.1
Ross, W.S.2
Romanovski, V.3
-
31
-
-
0029011701
-
A second 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., Jr., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules, J. Am. Chem. Soc. 117, 5179-5197.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz Jr., K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
32
-
-
0141688512
-
-
University of California, San Francisco
-
Case, D. A., Pearlman, D. A., Caldwell, J. W., Cheatham, T. E., II, Ross, W. S., Simmerling, C. L., Darden, T. A., Merz, K. M., Jr., Stanton, R. V., Cheng, A. L., Vincent, J. J., Crowley, M., Ferguson, D. M., Radmer, R. J., Seibel, G. L., Singh, U. C., Weiner, P. K., and Kollman, P. A. (2002) AMBER 7.0, University of California, San Francisco.
-
(2002)
AMBER 7.0
-
-
Case, D.A.1
Pearlman, D.A.2
Caldwell, J.W.3
Cheatham II, T.E.4
Ross, W.S.5
Simmerling, C.L.6
Darden, T.A.7
Merz Jr., K.M.8
Stanton, R.V.9
Cheng, A.L.10
Vincent, J.J.11
Crowley, M.12
Ferguson, D.M.13
Radmer, R.J.14
Seibel, G.L.15
Singh, U.C.16
Weiner, P.K.17
Kollman, P.A.18
-
33
-
-
33750587438
-
Molecular dynamics with coupling to and external bath
-
Berendsen, H. J. C., Potsma, J. P. M., van Gunsteren, W. F., DiNola, A. D., and Haak, J. R. (1984) Molecular dynamics with coupling to and external bath, J. Chem. Phys. 81, 3684-3690.
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Potsma, J.P.M.2
Van Gunsteren, W.F.3
DiNola, A.D.4
Haak, J.R.5
-
34
-
-
33645961739
-
A smooth particle-mesh-ewald method
-
Essman, V., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G. (1995) A smooth particle-mesh-ewald method, J. Chem. Phys. 103, 8577-8593.
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essman, V.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
35
-
-
0026244229
-
Molscript: A program to produce both detailed and schematic plots of protein structures
-
Kraulis, P. J. (1991) Molscript: A program to produce both detailed and schematic plots of protein structures, J. Appl. Crystallogr. 24, 946-950.
-
(1991)
J. Appl. Crystallogr.
, vol.24
, pp. 946-950
-
-
Kraulis, P.J.1
-
36
-
-
0030815133
-
Raster3d: Photorealistic molecular graphics
-
Merritt, E. A., and Bacon, D. J. (1997) Raster3d: Photorealistic molecular graphics, Methods Enzymol. 277, 505-524.
-
(1997)
Methods Enzymol.
, vol.277
, pp. 505-524
-
-
Merritt, E.A.1
Bacon, D.J.2
-
37
-
-
11644261806
-
Automated docking using a lamarckian genetic algorithm and empirical binding free energy function
-
Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., and Olson, A. J. (1998) Automated docking using a lamarckian genetic algorithm and empirical binding free energy function., J. Comput. Chem. 19, 1639-1662.
-
(1998)
J. Comput. Chem.
, vol.19
, pp. 1639-1662
-
-
Morris, G.M.1
Goodsell, D.S.2
Halliday, R.S.3
Huey, R.4
Hart, W.E.5
Belew, R.K.6
Olson, A.J.7
-
38
-
-
0025135112
-
Automated docking of substrates to proteins by simulated annealing
-
Goodsell, D. S., and Olson, A. J. (1990) Automated docking of substrates to proteins by simulated annealing, Proteins: Struct. Funct. Genet. 8, 195-202.
-
(1990)
Proteins: Struct. Funct. Genet.
, vol.8
, pp. 195-202
-
-
Goodsell, D.S.1
Olson, A.J.2
-
39
-
-
0142250488
-
Conformational properties of penicillins: Quantum chemical calculations and molecular dynamics simulations of benzylpenicillin
-
Díaz, N., Sordo, T. L., and Suárez, D. (2003) Conformational properties of penicillins: Quantum chemical calculations and molecular dynamics simulations of benzylpenicillin, J. Comput. Chem. 24, 1864-1873.
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1864-1873
-
-
Díaz, N.1
Sordo, T.L.2
Suárez, D.3
-
40
-
-
0003418036
-
-
(Yarkony, D. R., Ed.) World Scientific, Singapore
-
Becke, A. D. (1995) in Modern Electronic Structure Theory, Part II (Yarkony, D. R., Ed.) World Scientific, Singapore.
-
(1995)
Modern Electronic Structure Theory, Part II
-
-
Becke, A.D.1
-
41
-
-
14744277791
-
-
Schrödinger Inc., Portland, OR
-
JAGUAR, Schrödinger Inc., Portland, OR, 1991-2003.
-
(1991)
JAGUAR
-
-
-
42
-
-
0000304948
-
Accurate first principles calculation of molecular charge distributions and solvation energies from ab initio quantum mechanics and continuum dielectric theory
-
Tannor, D. J., Marten, B., Murphy, R., Friesner, R. A., Sitkoff, D., Nicholls, A., Ringnalda, M., Goddard, I., W. A., and Honig, B. (1994) Accurate first principles calculation of molecular charge distributions and solvation energies from ab initio quantum mechanics and continuum dielectric theory., J. Am. Chem. Soc. 116, 11875-11882.
-
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 11875-11882
-
-
Tannor, D.J.1
Marten, B.2
Murphy, R.3
Friesner, R.A.4
Sitkoff, D.5
Nicholls, A.6
Ringnalda, M.7
Goddard, I.8
Honig, B.9
-
43
-
-
84988129057
-
Optimization of parameters for semiempirical methods. I. Method
-
Stewart, J. J. P. (1989) Optimization of parameters for semiempirical methods. I. Method, J. Comput. Chem. 10, 209-220.
-
(1989)
J. Comput. Chem.
, vol.10
, pp. 209-220
-
-
Stewart, J.J.P.1
-
44
-
-
84962467100
-
Fully quantum mechanical description of proteins in solution. Combining linear scaling quantum mechanical methodologies with the Poisson-Boltzmann equation
-
Gogonea, V., and Merz, K. M., Jr. (1999) Fully quantum mechanical description of proteins in solution. Combining linear scaling quantum mechanical methodologies with the Poisson-Boltzmann equation, J. Phys. Chem. A 103, 5171-5178.
-
(1999)
J. Phys. Chem. A
, vol.103
, pp. 5171-5178
-
-
Gogonea, V.1
Merz Jr., K.M.2
-
45
-
-
0003839101
-
-
The Pennsylvania State University
-
Cheng, A., Stanton, R. S., Vincent, J. J., van der Vaart, A., Damodaran, K. V., Dixon, S. L., Hartsough, D. S., Mori, M., Best, S. A., Monard, G., Garcia, M., Van Zant, L. C., and Merz, K. M. J. (1999) ROAR 2.0, The Pennsylvania State University.
-
(1999)
ROAR 2.0
-
-
Cheng, A.1
Stanton, R.S.2
Vincent, J.J.3
Van Der Vaart, A.4
Damodaran, K.V.5
Dixon, S.L.6
Hartsough, D.S.7
Mori, M.8
Best, S.A.9
Monard, G.10
Garcia, M.11
Van Zant, L.C.12
Merz, K.M.J.13
-
46
-
-
0030710155
-
Electrostatic and non-electrostatic contributions to the binding free energies of anthracycline antibiotics to DNA
-
Baginski, M., Fogolari, F., and Briggs, J. M. (1997) Electrostatic and non-electrostatic contributions to the binding free energies of anthracycline antibiotics to DNA, J. Mol. Biol. 274, 253-267.
-
(1997)
J. Mol. Biol.
, vol.274
, pp. 253-267
-
-
Baginski, M.1
Fogolari, F.2
Briggs, J.M.3
-
47
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case, D. A., and Cheatham, T. E. (2000) Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models, Acc. Chem. Res. 33, 889-897.
-
(2000)
Acc. Chem. Res.
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
Donini, O.11
Cieplak, P.12
Srinivasan, J.13
Case, D.A.14
Cheatham, T.E.15
-
48
-
-
0347602124
-
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex ras-raf
-
Gohlke, H., and Case, D. A. (2003) Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex ras-raf, J. Comput. Chem. 25, 238-250.
-
(2003)
J. Comput. Chem.
, vol.25
, pp. 238-250
-
-
Gohlke, H.1
Case, D.A.2
-
49
-
-
0033246389
-
Linear scaling electronic structure methods
-
Goedecker, S. (1999) Linear scaling electronic structure methods, Rev. Mod. Phys. 71, 1085-1123.
-
(1999)
Rev. Mod. Phys.
, vol.71
, pp. 1085-1123
-
-
Goedecker, S.1
-
50
-
-
0043144732
-
A density-matrix form of the divide-and-conquer approach for electronic structure calculations of large molecules
-
Yang, W., and Lee, T.-S. (1995) A density-matrix form of the divide-and-conquer approach for electronic structure calculations of large molecules, J. Chem. Phys. 103, 5674-5678.
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 5674-5678
-
-
Yang, W.1
Lee, T.-S.2
-
51
-
-
0346506503
-
Fast, accurate semiempirical molecular orbital calculations for macromolecules
-
Dixon, S. L., and Merz, K. M., Jr. (1997) Fast, accurate semiempirical molecular orbital calculations for macromolecules, J. Chem. Phys. 107, 879-893.
-
(1997)
J. Chem. Phys.
, vol.107
, pp. 879-893
-
-
Dixon, S.L.1
Merz Jr., K.M.2
-
52
-
-
0000263008
-
Study of hydrogen bonding interactions relevant to biomolecular structure and function
-
Zheng, Y. J., and Merz, K. M., Jr. (1992) Study of hydrogen bonding interactions relevant to biomolecular structure and function, J. Comput. Chem. 13, 1161-1169.
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 1161-1169
-
-
Zheng, Y.J.1
Merz Jr., K.M.2
-
53
-
-
0000958036
-
New class IV charge model for extracting accurate partial charges from wave functions
-
Li, J., Cramer, C. J., and Truhlar, D. G. (1998) New class IV charge model for extracting accurate partial charges from wave functions, J. Phys. Chem. A. 102, 1820-1831.
-
(1998)
J. Phys. Chem. A
, vol.102
, pp. 1820-1831
-
-
Li, J.1
Cramer, C.J.2
Truhlar, D.G.3
-
54
-
-
0042041206
-
Uff, a full periodic table force field for molecular mechanics and molecular dynamics simulations
-
Rappé, A. K., Casewit, C. J., Colwell, K. S., Goddard, W. A., III, and Skiff, W. M. (1992) Uff, a full periodic table force field for molecular mechanics and molecular dynamics simulations, J. Am. Chem. Soc. 114, 10024-10035.
-
(1992)
J. Am. Chem. Soc.
, vol.114
, pp. 10024-10035
-
-
Rappé, A.K.1
Casewit, C.J.2
Colwell, K.S.3
Goddard III, W.A.4
Skiff, W.M.5
-
55
-
-
0003463895
-
-
The Pennsylvania State University
-
Dixon, S. L., van der Vaart, A., Gogonea, V., Vincent, J. J., Brothers, E. N., Suarez, D., Westerhoff, L. M., and Merz, K. M. J. (1999) DivCon99, The Pennsylvania State University.
-
(1999)
DivCon99
-
-
Dixon, S.L.1
Van Der Vaart, A.2
Gogonea, V.3
Vincent, J.J.4
Brothers, E.N.5
Suarez, D.6
Westerhoff, L.M.7
Merz, K.M.J.8
-
56
-
-
0343725680
-
Critical assessment of the performance of the semiempirical divide and conquer method for single point calculations and geometry optimizations of large chemical systems
-
van der Vaart, A., Suarez, D., and Merz, K. M., Jr. (2000) Critical assessment of the performance of the semiempirical divide and conquer method for single point calculations and geometry optimizations of large chemical systems, J. Chem. Phys. 113, 10512-10523.
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 10512-10523
-
-
Van Der Vaart, A.1
Suarez, D.2
Merz Jr., K.M.3
-
57
-
-
33646887390
-
On the limited memory BFGS method for large scale optimization
-
Lui, D. C., and Nocedal, J. (1989) On the limited memory BFGS method for large scale optimization, Math. Programming 45, 503-528.
-
(1989)
Math. Programming
, vol.45
, pp. 503-528
-
-
Lui, D.C.1
Nocedal, J.2
-
58
-
-
0033405041
-
Molecular dynamics and free energy calculations applied to affinity maturation in antibody 48G7
-
Chong, L. T., Duan, Y., Wang, L., Massova, I., and Kollman, P. A. (1999) Molecular dynamics and free energy calculations applied to affinity maturation in antibody 48G7, Proc. Natl. Acad. Sci. 96, 14330-14335.
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 14330-14335
-
-
Chong, L.T.1
Duan, Y.2
Wang, L.3
Massova, I.4
Kollman, P.A.5
-
59
-
-
0942276314
-
A quantum mechanics-based scoring function: Study of zinc ion-mediated ligand binding
-
Raha, K., and Merz, K. M., Jr. (2004) A quantum mechanics-based scoring function: Study of zinc ion-mediated ligand binding, J. Am. Chem. Soc. 126, 1020-1021.
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 1020-1021
-
-
Raha, K.1
Merz Jr., K.M.2
-
61
-
-
0013677216
-
The ability of the semiempirical PM3 method to model proton-transfer reactions in symmetric hydrogen bonded systems
-
Kallies, B., and Mitzner, R. (1995) The ability of the semiempirical PM3 method to model proton-transfer reactions in symmetric hydrogen bonded systems, J. Mol. Model. 1, 68-78.
-
(1995)
J. Mol. Model.
, vol.1
, pp. 68-78
-
-
Kallies, B.1
Mitzner, R.2
-
63
-
-
0034595512
-
The crystal structure of the penicillin-binding protein 2x from Streptococcus pneumoniae and its acyl-enzyme form: Implication in drug resistance
-
Gordon, E., Mouz, N., Duée, E., and Dideberg, O. (2000) The crystal structure of the penicillin-binding protein 2x from Streptococcus pneumoniae and its acyl-enzyme form: Implication in drug resistance, J. Mol. Biol. 299, 477-485.
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 477-485
-
-
Gordon, E.1
Mouz, N.2
Duée, E.3
Dideberg, O.4
-
64
-
-
0036829003
-
Structural basis for the beta-lactam resistance of pbp2a from methicillin-resistant Staphylococcus aureus
-
Lim, D., and Strynadka, N. C. (2002) Structural basis for the beta-lactam resistance of pbp2a from methicillin-resistant Staphylococcus aureus, Nat. Struct. Biol. 9, 870-876.
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 870-876
-
-
Lim, D.1
Strynadka, N.C.2
-
65
-
-
0347362788
-
Crystal structure of wild-type penicillin-binding protein 5 from Escherichia coli
-
Nicholas, R. A., Krings, S., Tomberg, J., Nicola, G., and Davies, C. (2003) Crystal structure of wild-type penicillin-binding protein 5 from Escherichia coli, J. Biol. Chem. 278, 52826-52833.
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 52826-52833
-
-
Nicholas, R.A.1
Krings, S.2
Tomberg, J.3
Nicola, G.4
Davies, C.5
-
66
-
-
0035943720
-
Kinetics of beta-lactam interactions with penicillin-susceptible and -resistant penicillin-binding protein 2x proteins from Streptococcus pneumoniae
-
Lu, W.-P., Kincaid, E., Sun, Y., and Bauer, M. D. (2001) Kinetics of beta-lactam interactions with penicillin-susceptible and -resistant penicillin-binding protein 2x proteins from Streptococcus pneumoniae, J. Biol. Chem. 276, 31494-31501.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 31494-31501
-
-
Lu, W.-P.1
Kincaid, E.2
Sun, Y.3
Bauer, M.D.4
-
67
-
-
0022460491
-
Streptomyces K15 DD-peptidase-catalysed reactions with ester and amide carbonyl donors
-
Nguyen-Distèche, M., Leyh-Bouille, M., Pirlot, S., Frère, J.-M., and Ghuysen, J.-M. (1986) Streptomyces K15 DD-peptidase-catalysed reactions with ester and amide carbonyl donors, Biochem. J. 235, 167-176.
-
(1986)
Biochem. J.
, vol.235
, pp. 167-176
-
-
Nguyen-Distèche, M.1
Leyh-Bouille, M.2
Pirlot, S.3
Frère, J.-M.4
Ghuysen, J.-M.5
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