-
1
-
-
79957445712
-
Porphyrins: One ring in the colors of life
-
Dayan FE, Dayan EA, (2011) Porphyrins: One ring in the colors of life. Am Sci 99: 236-243.
-
(2011)
Am Sci
, vol.99
, pp. 236-243
-
-
Dayan, F.E.1
Dayan, E.A.2
-
2
-
-
0016671103
-
The enzymic conversion of protoporphyrinogen IX to protoporphyrin IX. Protoporphyrinogen oxidase activity in mitochondrial extracts of Saccharomyces cerevisiae
-
Poulson R, Polglase WJ, (1975) The enzymic conversion of protoporphyrinogen IX to protoporphyrin IX. Protoporphyrinogen oxidase activity in mitochondrial extracts of Saccharomyces cerevisiae. J Biol Chem 250: 1269-1274.
-
(1975)
J Biol Chem
, vol.250
, pp. 1269-1274
-
-
Poulson, R.1
Polglase, W.J.2
-
3
-
-
0017070102
-
The enzymic conversion of protoporphyrinogen IX to protoporphyrin IX in mammalian mitochondria
-
Poulson R, (1976) The enzymic conversion of protoporphyrinogen IX to protoporphyrin IX in mammalian mitochondria. J Biol Chem 251: 3730-3733.
-
(1976)
J Biol Chem
, vol.251
, pp. 3730-3733
-
-
Poulson, R.1
-
4
-
-
33747589914
-
A codon deletion confers resistance to herbicides inhibiting protoporphyrinogen oxidase
-
Patzoldt WL, Hager AG, McCormick JS, Tranel PJ, (2006) A codon deletion confers resistance to herbicides inhibiting protoporphyrinogen oxidase. Proc Natl Acad Sci U S A 103: 12329-12334.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 12329-12334
-
-
Patzoldt, W.L.1
Hager, A.G.2
McCormick, J.S.3
Tranel, P.J.4
-
5
-
-
78049279741
-
Identification of a gene essential for protoporphyrinogen IX oxidase activity in the cyanobacterium Synechocystis sp. PCC6803
-
Kato K, Tanaka R, Sano S, Tanaka A, Hosaka H, (2010) Identification of a gene essential for protoporphyrinogen IX oxidase activity in the cyanobacterium Synechocystis sp. PCC6803. Proc Natl Acad Sci U S A 107: 16649-16654.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 16649-16654
-
-
Kato, K.1
Tanaka, R.2
Sano, S.3
Tanaka, A.4
Hosaka, H.5
-
6
-
-
0041662029
-
A point mutation of valine-311 to methionine in Bacillus subtilis protoporphyrinogen oxidase does not greatly increase resistance to the diphenyl ether herbicide oxyfluorfen
-
Jeong E, Houn T, Kuk Y, Kim ES, Chandru HK, et al. (2003) A point mutation of valine-311 to methionine in Bacillus subtilis protoporphyrinogen oxidase does not greatly increase resistance to the diphenyl ether herbicide oxyfluorfen. Bioorg Chem 31: 389-397.
-
(2003)
Bioorg Chem
, vol.31
, pp. 389-397
-
-
Jeong, E.1
Houn, T.2
Kuk, Y.3
Kim, E.S.4
Chandru, H.K.5
-
7
-
-
0141872474
-
Kinetic and physical characterisation of recombinant wild-type and mutant human protoporphyrinogen oxidases
-
Maneli MH, Corrigall AV, Klump HH, Davids LM, Kirsch RE, et al. (2003) Kinetic and physical characterisation of recombinant wild-type and mutant human protoporphyrinogen oxidases. Biochim Biophys Acta 1650: 10-21.
-
(2003)
Biochim Biophys Acta
, vol.1650
, pp. 10-21
-
-
Maneli, M.H.1
Corrigall, A.V.2
Klump, H.H.3
Davids, L.M.4
Kirsch, R.E.5
-
8
-
-
77952419950
-
Biochemical and structural consequences of a glycine deletion in the alpha-8 helix of protoporphyrinogen oxidase
-
Dayan FE, Daga PR, Duke SO, Lee RM, Tranel PJ, et al. (2010) Biochemical and structural consequences of a glycine deletion in the alpha-8 helix of protoporphyrinogen oxidase. Biochim Biophys Acta 1804: 1548-1556.
-
(2010)
Biochim Biophys Acta
, vol.1804
, pp. 1548-1556
-
-
Dayan, F.E.1
Daga, P.R.2
Duke, S.O.3
Lee, R.M.4
Tranel, P.J.5
-
9
-
-
0032167638
-
The domain structure of protoporphyrinogen oxidase, the molecular target of diphenyl ether-type herbicides
-
Arnould S, Camadro JM, (1998) The domain structure of protoporphyrinogen oxidase, the molecular target of diphenyl ether-type herbicides. Proc Natl Acad Sci U S A 95: 10553-10558.
-
(1998)
Proc Natl Acad Sci U S A
, vol.95
, pp. 10553-10558
-
-
Arnould, S.1
Camadro, J.M.2
-
10
-
-
0024970331
-
Protoporphyrinogen oxidase as a molecular target for diphenyl ether herbicides
-
Matringe M, Camadro JM, Labbe P, Scalla R, (1989) Protoporphyrinogen oxidase as a molecular target for diphenyl ether herbicides. Biochem J 260: 231-235.
-
(1989)
Biochem J
, vol.260
, pp. 231-235
-
-
Matringe, M.1
Camadro, J.M.2
Labbe, P.3
Scalla, R.4
-
11
-
-
9644290818
-
Synthesis and herbicidal activity of novel heterocyclic protoporphyrinogen oxidase inhibitors
-
Meazza G, Bettarini F, La Porta P, Piccardi P, Signorini E, et al. (2004) Synthesis and herbicidal activity of novel heterocyclic protoporphyrinogen oxidase inhibitors. Pest Manag Sci 60: 1178-1188.
-
(2004)
Pest Manag Sci
, vol.60
, pp. 1178-1188
-
-
Meazza, G.1
Bettarini, F.2
La Porta, P.3
Piccardi, P.4
Signorini, E.5
-
13
-
-
70449642877
-
Photofrin PDT for early stage oesophageal cancer: long term results in 40 patients and literature review
-
Moghissi K, Dixon K, Stringer M, Thorpe JA, (2009) Photofrin PDT for early stage oesophageal cancer: long term results in 40 patients and literature review. Photodiagnosis Photodyn Ther 6: 159-166.
-
(2009)
Photodiagnosis Photodyn Ther
, vol.6
, pp. 159-166
-
-
Moghissi, K.1
Dixon, K.2
Stringer, M.3
Thorpe, J.A.4
-
14
-
-
67349201695
-
Photodynamic therapy (PDT): a short review on cellular mechanisms and cancer research applications for PDT
-
Robertson CA, Evans DH, Abrahamse H, (2009) Photodynamic therapy (PDT): a short review on cellular mechanisms and cancer research applications for PDT. J Photochem Photobiol B 96: 1-8.
-
(2009)
J Photochem Photobiol B
, vol.96
, pp. 1-8
-
-
Robertson, C.A.1
Evans, D.H.2
Abrahamse, H.3
-
16
-
-
33644938813
-
Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain
-
Zhang D, Gullingsrud J, McCammon JA, (2006) Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain. J Am Chem Soc 128: 3019-3026.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 3019-3026
-
-
Zhang, D.1
Gullingsrud, J.2
McCammon, J.A.3
-
17
-
-
79960007037
-
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
-
Buch I, Giorgino T, De Fabritiis G, (2011) Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proc Natl Acad Sci U S A 108: 10184-10189.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 10184-10189
-
-
Buch, I.1
Giorgino, T.2
De Fabritiis, G.3
-
19
-
-
2442563409
-
Crystal structure of protoporphyrinogen IX oxidase: a key enzyme in haem and chlorophyll biosynthesis
-
Koch M, Breithaupt C, Kiefersauer R, Freigang J, Huber R, et al. (2004) Crystal structure of protoporphyrinogen IX oxidase: a key enzyme in haem and chlorophyll biosynthesis. EMBO J 23: 1720-1728.
-
(2004)
EMBO J
, vol.23
, pp. 1720-1728
-
-
Koch, M.1
Breithaupt, C.2
Kiefersauer, R.3
Freigang, J.4
Huber, R.5
-
20
-
-
33947230298
-
Functional definition of the tobacco protoporphyrinogen IX oxidase substrate-binding site
-
Heinemann IU, Diekmann N, Masoumi A, Koch M, Messerschmidt A, et al. (2007) Functional definition of the tobacco protoporphyrinogen IX oxidase substrate-binding site. Biochem J 402: 575-580.
-
(2007)
Biochem J
, vol.402
, pp. 575-580
-
-
Heinemann, I.U.1
Diekmann, N.2
Masoumi, A.3
Koch, M.4
Messerschmidt, A.5
-
21
-
-
79551625890
-
Structural insight into human variegate porphyria disease
-
Qin X, Tan Y, Wang L, Wang Z, Wang B, et al. (2010) Structural insight into human variegate porphyria disease. FASEB J 25: 653-664.
-
(2010)
FASEB J
, vol.25
, pp. 653-664
-
-
Qin, X.1
Tan, Y.2
Wang, L.3
Wang, Z.4
Wang, B.5
-
22
-
-
79955983984
-
Structure-activity relationships of diphenyl-ether as protoporphyrinogen oxidase inhibitors: insights from computational simulations
-
Hao GF, Tan Y, Yu NX, Yang GF, (2011) Structure-activity relationships of diphenyl-ether as protoporphyrinogen oxidase inhibitors: insights from computational simulations. J Comput Aided Mol Des 25: 213-222.
-
(2011)
J Comput Aided Mol Des
, vol.25
, pp. 213-222
-
-
Hao, G.F.1
Tan, Y.2
Yu, N.X.3
Yang, G.F.4
-
23
-
-
80053106260
-
Human butyrylcholinesterase-cocaine binding pathway and free energy profiles by molecular dynamics and potential of mean force simulations
-
Huang X, Zheng F, Zhan CG, (2011) Human butyrylcholinesterase-cocaine binding pathway and free energy profiles by molecular dynamics and potential of mean force simulations. J Phys Chem B 115: 11254-11260.
-
(2011)
J Phys Chem B
, vol.115
, pp. 11254-11260
-
-
Huang, X.1
Zheng, F.2
Zhan, C.G.3
-
24
-
-
84863834582
-
Computational discovery of picomolar Q(o) site inhibitors of cytochrome bc1 complex
-
Hao GF, Wang F, Li H, Zhu XL, Yang WC, et al. (2012) Computational discovery of picomolar Q(o) site inhibitors of cytochrome bc1 complex. J Am Chem Soc 134: 11168-11176.
-
(2012)
J Am Chem Soc
, vol.134
, pp. 11168-11176
-
-
Hao, G.F.1
Wang, F.2
Li, H.3
Zhu, X.L.4
Yang, W.C.5
-
25
-
-
37049059539
-
Prevalence and significance of the product inhibition of enzymes
-
Frieden E, Walter C, (1963) Prevalence and significance of the product inhibition of enzymes. Nature 198: 834-837.
-
(1963)
Nature
, vol.198
, pp. 834-837
-
-
Frieden, E.1
Walter, C.2
-
26
-
-
74349118194
-
GDP-mannose pyrophosphorylase is essential in the bloodstream form of Trypanosoma brucei
-
Denton H, Fyffe S, Smith TK, (2010) GDP-mannose pyrophosphorylase is essential in the bloodstream form of Trypanosoma brucei. Biochem J 425: 603-614.
-
(2010)
Biochem J
, vol.425
, pp. 603-614
-
-
Denton, H.1
Fyffe, S.2
Smith, T.K.3
-
27
-
-
70349376092
-
Two forms of feedback inhibition determine the dynamical state of a small hippocampal network
-
Zeldenrust F, Wadman WJ (2009) Two forms of feedback inhibition determine the dynamical state of a small hippocampal network. Neural Netw. 1139-1158.
-
(2009)
Neural Netw
, pp. 1139-1158
-
-
Zeldenrust, F.1
Wadman, W.J.2
-
28
-
-
0038626673
-
-
revision B-03: Gaussian, Inc.: Pittsburgh, PA
-
Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, et al. (2003) Gaussian 03, revision B-03: Gaussian, Inc.: Pittsburgh, PA.
-
(2003)
Gaussian 03
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
-
29
-
-
33947716119
-
A semiempirical free energy force field with charge-based desolvation
-
Huey R, Morris GM, Olson AJ, Goodsell DS, (2007) A semiempirical free energy force field with charge-based desolvation. J Comput Chem 28: 1145-1152.
-
(2007)
J Comput Chem
, vol.28
, pp. 1145-1152
-
-
Huey, R.1
Morris, G.M.2
Olson, A.J.3
Goodsell, D.S.4
-
30
-
-
14844293471
-
A component-based software environment for visualizing large macromolecular assemblies
-
Sanner MF, (2005) A component-based software environment for visualizing large macromolecular assemblies. Structure 13: 447-462.
-
(2005)
Structure
, vol.13
, pp. 447-462
-
-
Sanner, M.F.1
-
31
-
-
72149124987
-
-
Case DA, Darden TA, Cheatham TE, Simmerling CL, Wang J, et al. (2006) AMBER 9: University of California: San Francisco.
-
(2006)
AMBER 9: University of California: San Francisco
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.E.3
Simmerling, C.L.4
Wang, J.5
-
32
-
-
84986468608
-
An approach to computing electrostatic charges for molecules
-
Singh UC, Kollman PA, (1984) An approach to computing electrostatic charges for molecules. J Comput Chem 5: 129-145.
-
(1984)
J Comput Chem
, vol.5
, pp. 129-145
-
-
Singh, U.C.1
Kollman, P.A.2
-
33
-
-
84986492477
-
Atomic charges derived from semiempirical methods
-
Besler BH, Merz KM, Kollman PA, (1990) Atomic charges derived from semiempirical methods. J Comput Chem 11: 431-439.
-
(1990)
J Comput Chem
, vol.11
, pp. 431-439
-
-
Besler, B.H.1
Merz, K.M.2
Kollman, P.A.3
-
34
-
-
3042524904
-
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
-
Bayly CI, Cieplak P, Cornell WD, Kollman PA, (1993) A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J Phys Chem 97: 10269-10280.
-
(1993)
J Phys Chem
, vol.97
, pp. 10269-10280
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.D.3
Kollman, P.A.4
-
35
-
-
0000667030
-
Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation
-
Cornell WD, Cieplak P, Bayly CI, Kollman PA, (1993) Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation. J Am Chem Soc 115: 9620-9631.
-
(1993)
J Am Chem Soc
, vol.115
, pp. 9620-9631
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Kollman, P.A.4
-
36
-
-
65249103492
-
Understanding the mechanism of drug resistance due to a codon deletion in protoporphyrinogen oxidase through computational modeling
-
Hao GF, Zhu XL, Ji FQ, Zhang L, Yang GF, et al. (2009) Understanding the mechanism of drug resistance due to a codon deletion in protoporphyrinogen oxidase through computational modeling. J Phys Chem B 113: 4865-4875.
-
(2009)
J Phys Chem B
, vol.113
, pp. 4865-4875
-
-
Hao, G.F.1
Zhu, X.L.2
Ji, F.Q.3
Zhang, L.4
Yang, G.F.5
-
37
-
-
0034702646
-
Fluctuation formulas in molecular-dynamics simulations with the weak coupling heat bath
-
Morishita T, (2000) Fluctuation formulas in molecular-dynamics simulations with the weak coupling heat bath. J Chem Phys 113: 2976-2982.
-
(2000)
J Chem Phys
, vol.113
, pp. 2976-2982
-
-
Morishita, T.1
-
38
-
-
33846823909
-
Particle mesh Ewald: An N. log(N) method for Ewald sums in large systems
-
Darden T, York D, Pedersen L, (1993) Particle mesh Ewald: An N. log(N) method for Ewald sums in large systems. J Chem Phys 98: 10089-10092.
-
(1993)
J Chem Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
40
-
-
33646940952
-
Numerical integration of the Cartesian equations of mot ion of a system with constraints: molecular dynamics of n-alkanes
-
Ryckaert JP, Ciccotti G, Berendsen HJC, (1977) Numerical integration of the Cartesian equations of mot ion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23: 327-341.
-
(1977)
J Comput Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
41
-
-
0034521981
-
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models
-
Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, et al. (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
-
42
-
-
77954949788
-
Computational mutation scanning and drug resistance mechanisms of HIV-1 protease inhibitors
-
Hao GF, Yang GF, Zhan CG, (2010) Computational mutation scanning and drug resistance mechanisms of HIV-1 protease inhibitors. J Phys Chem B 114: 9663-9676.
-
(2010)
J Phys Chem B
, vol.114
, pp. 9663-9676
-
-
Hao, G.F.1
Yang, G.F.2
Zhan, C.G.3
-
43
-
-
77956288365
-
The role of Phe82 and Phe351 in auxin-induced substrate perception by TIR1 ubiquitin ligase: a novel insight from molecular dynamics simulations
-
Hao GF, Yang GF, (2010) The role of Phe82 and Phe351 in auxin-induced substrate perception by TIR1 ubiquitin ligase: a novel insight from molecular dynamics simulations. PLoS One 5: e10742.
-
(2010)
PLoS One
, vol.5
-
-
Hao, G.F.1
Yang, G.F.2
-
44
-
-
0342929614
-
Nonphysical sampling distribution in Monte Carlo free-energy estimation: umbrella sampling
-
Torrie GM, Valleau JP, (1977) Nonphysical sampling distribution in Monte Carlo free-energy estimation: umbrella sampling. J Comput Phys 23: 187-199.
-
(1977)
J Comput Phys
, vol.23
, pp. 187-199
-
-
Torrie, G.M.1
Valleau, J.P.2
-
45
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules. I: The method
-
Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg J, (1992) The weighted histogram analysis method for free-energy calculations on biomolecules. I: The method. J Comput Chem 13: 1011-1021.
-
(1992)
J Comput Chem
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.5
-
46
-
-
28044458963
-
Computational redesign of human butyrylcholinesterase for anticocaine medication
-
Pan Y, Gao D, Yang W, Cho H, Yang G, et al. (2005) Computational redesign of human butyrylcholinesterase for anticocaine medication. Proc Natl Acad Sci U S A 102: 16656-16661.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 16656-16661
-
-
Pan, Y.1
Gao, D.2
Yang, W.3
Cho, H.4
Yang, G.5
-
47
-
-
31044435861
-
Computational design of a human butyrylcholinesterase mutant for accelerating cocaine hydrolysis based on the transition-state simulation
-
Gao D, Cho H, Yang W, Pan Y, Yang G, et al. (2006) Computational design of a human butyrylcholinesterase mutant for accelerating cocaine hydrolysis based on the transition-state simulation. Angew Chem-Int Edit 45: 653-657.
-
(2006)
Angew Chem -Int Edit
, vol.45
, pp. 653-657
-
-
Gao, D.1
Cho, H.2
Yang, W.3
Pan, Y.4
Yang, G.5
-
48
-
-
42149093718
-
Modeling the catalysis of anti-cocaine catalytic antibody: competing reaction pathways and free energy barriers
-
Pan Y, Gao D, Zhan CG, (2008) Modeling the catalysis of anti-cocaine catalytic antibody: competing reaction pathways and free energy barriers. J Am Chem Soc 130: 5140-5149.
-
(2008)
J Am Chem Soc
, vol.130
, pp. 5140-5149
-
-
Pan, Y.1
Gao, D.2
Zhan, C.G.3
|