-
1
-
-
33745334012
-
The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography
-
Wille G, Meyer D, Steinmetz A, Hinze E, Golbik R, Tittmann K (2006) The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography. Nat Chem Biol 2:390-490
-
(2006)
Nat Chem Biol
, vol.2
, pp. 390-490
-
-
Wille, G.1
Meyer, D.2
Steinmetz, A.3
Hinze, E.4
Golbik, R.5
Tittmann, K.6
-
2
-
-
64149099325
-
Reaction mechanisms of thiamin diphosphate enzymes: Defining states of ionization and tautomerization of the cofactor at individual steps
-
Nemeria NS, Chakraborty S, Balakrishnan A, Jordan F (2009) Reaction mechanisms of thiamin diphosphate enzymes: defining states of ionization and tautomerization of the cofactor at individual steps. FEBS J 276:2432-2446
-
(2009)
FEBS J
, vol.276
, pp. 2432-2446
-
-
Nemeria, N.S.1
Chakraborty, S.2
Balakrishnan, A.3
Jordan, F.4
-
3
-
-
58149293414
-
Designing the substrate specificity of D-hydantoinase using a rational approach
-
Lee SC, Chang YJ, Shin DM, Han J, Seo MH, Fazelinia H, Maranas CD, Kim HS (2009) Designing the substrate specificity of D-hydantoinase using a rational approach. Enzym Microb Technol 44:170-175
-
(2009)
Enzym Microb Technol
, vol.44
, pp. 170-175
-
-
Lee, S.C.1
Chang, Y.J.2
Shin, D.M.3
Han, J.4
Seo, M.H.5
Fazelinia, H.6
Maranas, C.D.7
Kim, H.S.8
-
4
-
-
33947672445
-
Extending Iterative Protein Redesign and Optimization (IPRO) in protein library design for ligand specificity
-
DOI 10.1529/biophysj.106.096016
-
Fazelinia H, Cirino PC, Maranas CD (2007) Extending iterative protein redesign and optimization (IPRO) in protein library design for ligand specificity. Biophys J 92:2120-2130 (Pubitemid 46495273)
-
(2007)
Biophysical Journal
, vol.92
, Issue.6
, pp. 2120-2130
-
-
Fazelinia, H.1
Cirino, P.C.2
Maranas, C.D.3
-
5
-
-
51849142353
-
Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis
-
Senger RS, Papoutsakis ET (2008) Genome-scale model for Clostridium acetobutylicum: part I. Metabolic network resolution and analysis. Biotechnol Bioeng 101:1036-1052
-
(2008)
Biotechnol Bioeng
, vol.101
, pp. 1036-1052
-
-
Senger, R.S.1
Papoutsakis, E.T.2
-
6
-
-
51849157931
-
Genome-scale model for Clostridium acetobutylicum: Part II. Development of specific proton flux states and numerically determined sub-systems
-
Senger RS, Papoutsakis ET (2008) Genome-scale model for Clostridium acetobutylicum: part II. Development of specific proton flux states and numerically determined sub-systems. Biotechnol Bioeng 101:1053-1071
-
(2008)
Biotechnol Bioeng
, vol.101
, pp. 1053-1071
-
-
Senger, R.S.1
Papoutsakis, E.T.2
-
7
-
-
51849115840
-
Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network
-
Lee J, Yun H, Feist AM, Palsson BO, Lee SY (2008) Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network. Appl Microbiol Biotechnol 80:849-862
-
(2008)
Appl Microbiol Biotechnol
, vol.80
, pp. 849-862
-
-
Lee, J.1
Yun, H.2
Feist, A.M.3
Palsson, B.O.4
Lee, S.Y.5
-
8
-
-
33846910173
-
Global reconstruction of the human metabolic network based on genomic and bibliomic data
-
DOI 10.1073/pnas.0610772104
-
Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BO (2007) Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci USA 104:1777-1782 (Pubitemid 46239855)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.6
, pp. 1777-1782
-
-
Duarte, N.C.1
Becker, S.A.2
Jamshidi, N.3
Thiele, I.4
Mo, M.L.5
Vo, T.D.6
Srivas, R.7
Palsson, B.O.8
-
9
-
-
34547809313
-
A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data
-
Thomas R, Paredes CJ, Mehrotra S, Hatzimanikatis V, Papoutsakis ET (2007) A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data. BMC Bioinformatics 8:228-236
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 228-236
-
-
Thomas, R.1
Paredes, C.J.2
Mehrotra, S.3
Hatzimanikatis, V.4
Papoutsakis, E.T.5
-
10
-
-
58149476770
-
OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold
-
Fazelinia H, Cirino PC, Maranas CD (2009) OptGraft: a computational procedure for transferring a binding site onto an existing protein scaffold. Protein Sci 18:180-195
-
(2009)
Protein Sci
, vol.18
, pp. 180-195
-
-
Fazelinia, H.1
Cirino, P.C.2
Maranas, C.D.3
-
11
-
-
34347258175
-
Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox
-
DOI 10.1038/nprot.2007.99, PII NPROT.2007.99
-
Becker SA, Feist AM, Mo ML, Hannum G, Palsson BO, Herrgard MJ (2007) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc 2:727-738 (Pubitemid 47040034)
-
(2007)
Nature Protocols
, vol.2
, Issue.3
, pp. 727-738
-
-
Becker, S.A.1
Feist, A.M.2
Mo, M.L.3
Hannum, G.4
Palsson, B.O.5
Herrgard, M.J.6
-
12
-
-
58549108388
-
Reconstruction of biochemical networks in microorganisms
-
Feist AM, Herrgard MJ, Thiele I, Reed JL, Palsson BO (2009) Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol 7:129-143
-
(2009)
Nat Rev Microbiol
, vol.7
, pp. 129-143
-
-
Feist, A.M.1
Herrgard, M.J.2
Thiele, I.3
Reed, J.L.4
Palsson, B.O.5
-
13
-
-
8744251043
-
Computational discovery of biochemical routes to specialty chemicals
-
DOI 10.1016/j.ces.2004.09.021, PII S0009250904006669, ISCRE18
-
Li CH, Henry CS, Jankowski MD, Ionita JA, Hatzimanikatis V, Broadbelt LJ (2004) Computational discovery of biochemical routes to specialty chemicals. Chem Eng Sci 59:5051-5060 (Pubitemid 39605747)
-
(2004)
Chemical Engineering Science
, vol.59
, Issue.22-23
, pp. 5051-5060
-
-
Li, C.1
Henry, C.S.2
Jankowski, M.D.3
Ionita, J.A.4
Hatzimanikatis, V.5
Broadbelt, L.J.6
-
14
-
-
17444382016
-
Exploring the diversity of complex metabolic networks
-
DOI 10.1093/bioinformatics/bti213
-
Hatzimanikatis V, Li CH, Ionita JA, Henry CS, Jankowski MD, Broadbelt LJ (2005) Exploring the diversity of complex metabolic networks. Bioinformatics 21:1603-1609 (Pubitemid 40542718)
-
(2005)
Bioinformatics
, vol.21
, Issue.8
, pp. 1603-1609
-
-
Hatzimanikatis, V.1
Li, C.2
Ionita, J.A.3
Henry, C.S.4
Jankowski, M.D.5
Broadbelt, L.6
-
17
-
-
0028727474
-
Computer generated reaction networks: On-the-fly calculation of species properties using computational quantum chemistry
-
Broadbelt LJ, Stark SM, Klein MT (1994) Computer generated reaction networks: on-the-fly calculation of species properties using computational quantum chemistry. Chem Eng Sci 49:4991-5010
-
(1994)
Chem Eng Sci
, vol.49
, pp. 4991-5010
-
-
Broadbelt, L.J.1
Stark, S.M.2
Klein, M.T.3
-
18
-
-
0028410110
-
Computer-generated pyrolysis modeling - On-the-fly generation of species, reactions, and rates
-
Broadbelt LJ, Stark SM, Klein MT (1994) Computer-generated pyrolysis modeling - on-the-fly generation of species, reactions, and rates. Ind Eng Chem Res 33:790-799
-
(1994)
Ind Eng Chem Res
, vol.33
, pp. 790-799
-
-
Broadbelt, L.J.1
Stark, S.M.2
Klein, M.T.3
-
19
-
-
0000670212
-
Termination of computer-generated reaction-mechanisms - Species rank-based convergence criterion
-
Broadbelt LJ, Stark SM, Klein MT (1995) Termination of computer-generated reaction-mechanisms - species rank-based convergence criterion. Ind Eng Chem Res 34:2566-2573
-
(1995)
Ind Eng Chem Res
, vol.34
, pp. 2566-2573
-
-
Broadbelt, L.J.1
Stark, S.M.2
Klein, M.T.3
-
20
-
-
22144436255
-
Theoretical considerations and computational analysis of the complexity in polyketide synthesis pathways
-
DOI 10.1021/ja051586y
-
Gonzalez-Lergier J, Broadbelt LJ, Hatzimanikatis V (2005) Theoretical considerations and computational analysis of the complexity in polyketide synthesis pathways. J Am Chem Soc 127:9930-9938 (Pubitemid 40981557)
-
(2005)
Journal of the American Chemical Society
, vol.127
, Issue.27
, pp. 9930-9938
-
-
Gonzalez-Lergier, J.1
Broadbelt, L.J.2
Hatzimanikatis, V.3
-
21
-
-
77953578214
-
Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate
-
Henry CS, Broadbelt LJ, Hatzimanikatis V (2010) Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate. Biotechnol Bioeng 106:462-473
-
(2010)
Biotechnol Bioeng
, vol.106
, pp. 462-473
-
-
Henry, C.S.1
Broadbelt, L.J.2
Hatzimanikatis, V.3
-
22
-
-
2642513030
-
Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space
-
DOI 10.1016/j.jtbi.2004.02.006, PII S0022519304000554
-
Wiback SJ, Famili I, Greenberg HJ, Palsson BØ (2004) Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space. J Theor Biol 228:437-447 (Pubitemid 38726066)
-
(2004)
Journal of Theoretical Biology
, vol.228
, Issue.4
, pp. 437-447
-
-
Wiback, S.J.1
Famili, I.2
Greenberg, H.J.3
Palsson, B.O.4
-
23
-
-
34347332311
-
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
-
Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3:131
-
(2007)
Mol Syst Biol
, vol.3
, pp. 131
-
-
Feist, A.M.1
Henry, C.S.2
Reed, J.L.3
Krummenacker, M.4
Joyce, A.R.5
Karp, P.D.6
Broadbelt, L.J.7
Hatzimanikatis, V.8
Palsson, B.O.9
-
24
-
-
33847797256
-
Thermodynamics-based metabolic flux analysis
-
DOI 10.1529/biophysj.106.093138
-
Henry CS, Broadbelt LJ, Hatzimanikatis V (2007) Thermodynamics-based metabolic flux analysis. Biophys J 92:1792-1805 (Pubitemid 46393490)
-
(2007)
Biophysical Journal
, vol.92
, Issue.5
, pp. 1792-1805
-
-
Henry, C.S.1
Broadbelt, L.J.2
Hatzimanikatis, V.3
-
25
-
-
51049107514
-
Group contribution method for thermodynamic analysis of complex metabolic networks
-
Jankowski MD, Henry CS, Broadbelt LJ, Hatzimanikatis V (2008) Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys J 95:1487-1499
-
(2008)
Biophys J
, vol.95
, pp. 1487-1499
-
-
Jankowski, M.D.1
Henry, C.S.2
Broadbelt, L.J.3
Hatzimanikatis, V.4
-
26
-
-
1542269174
-
Acetone butanol ethanol (ABE) production from concentrated substrate: Reduction in substrate inhibition by fed-batch technique and product inhibition by gas stripping
-
DOI 10.1007/s00253-003-1400-x
-
Ezeji TC, Qureshi N, Blaschek HP (2004) Acetone butanol ethanol (ABE) production from concentrated substrate: reduction in substrate inhibition by fed-batch technique and product inhibition by gas stripping. Appl Microbiol Biotechnol 63:653-658 (Pubitemid 38316691)
-
(2004)
Applied Microbiology and Biotechnology
, vol.63
, Issue.6
, pp. 653-658
-
-
Ezeji, T.C.1
Qureshi, N.2
Blaschek, H.P.3
-
27
-
-
34249981232
-
Bioproduction of butanol from biomass: From genes to bioreactors
-
DOI 10.1016/j.copbio.2007.04.002, PII S0958166907000511, Energy biotechnology / Environmental biotechnology
-
Ezeji TC, Qureshi N, Blaschek HP (2007) Bioproduction of butanol from biomass: from genes to bioreactors. Curr Opin Biotechnol 18:220-227 (Pubitemid 46887658)
-
(2007)
Current Opinion in Biotechnology
, vol.18
, Issue.3
, pp. 220-227
-
-
Ezeji, T.C.1
Qureshi, N.2
Blaschek, H.P.3
-
28
-
-
2242456844
-
Glucose Uptake in Clostridium beijerinckii NCIMB 8052 and the Solvent-Hyperproducing Mutant BA101
-
Lee J, Blaschek HP (2001) Glucose uptake in Clostridium beijerinckii NCIMB 8052 and the solvent-hyperproducing mutant BA101. Appl Environ Microbiol 67:5025-5031 (Pubitemid 33701265)
-
(2001)
Applied and Environmental Microbiology
, vol.67
, Issue.3-12
, pp. 5025-5031
-
-
Lee, J.1
Blaschek, H.P.2
-
29
-
-
0034879273
-
Review of the enzymes and metabolic pathways (EMP) database
-
DOI 10.1006/mben.2001.0189
-
Burgard AP, Maranas CD (2001) Review of the Enzymes and Metabolic Pathways (EMP) Database. Metab Eng 3:193-194 (Pubitemid 32748162)
-
(2001)
Metabolic Engineering
, vol.3
, Issue.3
, pp. 193-194
-
-
Burgard, A.P.1
Maranas, C.D.2
-
30
-
-
64149111838
-
Reaction mechanisms of thiamin diphosphate enzymes: Redox reactions
-
Tittmann K (2009) Reaction mechanisms of thiamin diphosphate enzymes: redox reactions. FEBS J 276:2454-2468
-
(2009)
FEBS J
, vol.276
, pp. 2454-2468
-
-
Tittmann, K.1
-
31
-
-
36849091110
-
The enamine intermediate may not be universal to thiamine catalysis
-
DOI 10.1002/anie.200702993
-
Amara P, Fdez Galván I, Fontecilla-Camps JC, Field MJ (2007) The enamine intermediate may not be universal to thiamine catalysis. Angew Chem Int Ed 46:9019-9022 (Pubitemid 350232758)
-
(2007)
Angewandte Chemie - International Edition
, vol.46
, Issue.47
, pp. 9019-9022
-
-
Amara, P.1
Fdez, G.I.2
Fontecilla-Camps, J.C.3
Field, M.J.4
-
32
-
-
0010505580
-
Theoretical studies on the decarboxylation reaction in thiamin catalysis
-
Friedemann R, Breitkopf C (1996) Theoretical studies on the decarboxylation reaction in thiamin catalysis. Int J Quantum Chem 57:943-948 (Pubitemid 126534833)
-
(1996)
International Journal of Quantum Chemistry
, vol.57
, Issue.5
, pp. 943-948
-
-
Friedemann, R.1
Breitkopf, C.2
-
33
-
-
0037493009
-
Ab initio and DFT calculations on the initial step in thiamin catalysis
-
Friedemann R, Naumann S (2003) Ab initio and DFT calculations on the initial step in thiamin catalysis. J Mol Struct Theochem 630:275-281
-
(2003)
J Mol Struct Theochem
, vol.630
, pp. 275-281
-
-
Friedemann, R.1
Naumann, S.2
-
35
-
-
56849087272
-
Catalyzing separation of carbon dioxide in thiamin diphosphate-promoted decarboxylation
-
Kluger R, Rathgeber S (2008) Catalyzing separation of carbon dioxide in thiamin diphosphate-promoted decarboxylation. FEBS J 275:6089-6100
-
(2008)
FEBS J
, vol.275
, pp. 6089-6100
-
-
Kluger, R.1
Rathgeber, S.2
-
36
-
-
77952411134
-
Studying enzyme-substrate specificity in silico: A case study of the Escherichia coli glycolysis pathway
-
Kalyanaraman C, Jacobson MP (2010) Studying enzyme-substrate specificity in silico: a case study of the Escherichia coli glycolysis pathway. Biochemistry 49:4003-4005
-
(2010)
Biochemistry
, vol.49
, pp. 4003-4005
-
-
Kalyanaraman, C.1
Jacobson, M.P.2
-
38
-
-
70449634957
-
Predicting new molecular targets for known drugs
-
Keiser MJ, Setola V, Irwin JJ, Laggner C, Abbas AI, Hufeisen SJ, Jensen NH, Kuijer MB, Matos RC, Tran TB, Whaley R, Glennon RA, Hert J, Thomas KLH, Edwards DD, Shoichet BK, Roth BL (2009) Predicting new molecular targets for known drugs. Nature 462:175-181
-
(2009)
Nature
, vol.462
, pp. 175-181
-
-
Keiser, M.J.1
Setola, V.2
Irwin, J.J.3
Laggner, C.4
Abbas, A.I.5
Hufeisen, S.J.6
Jensen, N.H.7
Kuijer, M.B.8
Matos, R.C.9
Tran, T.B.10
Whaley, R.11
Glennon, R.A.12
Hert, J.13
Thomas, K.L.H.14
Edwards, D.D.15
Shoichet, B.K.16
Roth, B.L.17
-
39
-
-
3543002852
-
Ligand selectivity and competition between enzymes in silico
-
DOI 10.1038/nbt999
-
Macchiarulo A, Nobeli I, Thornton JM (2004) Ligand selectivity and competition between enzymes in silico. Nat Biotechnol 22:1039-1045 (Pubitemid 39014486)
-
(2004)
Nature Biotechnology
, vol.22
, Issue.8
, pp. 1039-1045
-
-
Macchiarulo, A.1
Nobeli, I.2
Thornton, J.M.3
-
41
-
-
12644303230
-
The enolase superfamily: A general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids
-
DOI 10.1021/bi9616413
-
Babbitt PC, Hasson MS, Wedekind JE, Palmer DRJ, Barrett WC, Reed GH, Rayment I, Ringe D, Kenyon GL, Gerlt JA (1996) The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids. Biochemistry 35:16489-16501 (Pubitemid 27020490)
-
(1996)
Biochemistry
, vol.35
, Issue.51
, pp. 16489-16501
-
-
Babbitt, P.C.1
Hasson, M.S.2
Wedekind, J.E.3
Palmer, D.R.J.4
Barrett, W.C.5
Reed, G.H.6
Rayment, I.7
Ringe, D.8
Kenyon, G.L.9
Gerlt, J.A.10
-
42
-
-
31544450787
-
Novel procedure for modeling ligand/receptor induced fit effects
-
DOI 10.1021/jm050540c
-
Sherman W, Day T, Jacobson MP, Friesner RA, Farid R (2006) Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem 49:534-553 (Pubitemid 43157487)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.2
, pp. 534-553
-
-
Sherman, W.1
Day, T.2
Jacobson, M.P.3
Friesner, R.A.4
Farid, R.5
-
43
-
-
12144289984
-
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
-
DOI 10.1021/jm0306430
-
Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47:1739-1749 (Pubitemid 38380917)
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.7
, pp. 1739-1749
-
-
Friesner, R.A.1
Banks, J.L.2
Murphy, R.B.3
Halgren, T.A.4
Klicic, J.J.5
Mainz, D.T.6
Repasky, M.P.7
Knoll, E.H.8
Shelley, M.9
Perry, J.K.10
Shaw, D.E.11
Francis, P.12
Shenkin, P.S.13
-
44
-
-
1642310340
-
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening
-
DOI 10.1021/jm030644s
-
Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, Banks JL (2004) Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 47:1750-1759 (Pubitemid 38380918)
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.7
, pp. 1750-1759
-
-
Halgren, T.A.1
Murphy, R.B.2
Friesner, R.A.3
Beard, H.S.4
Frye, L.L.5
Pollard, W.T.6
Banks, J.L.7
-
45
-
-
0032929940
-
Crystal structures of the key anaerobic enzyme pyruvate ferredoxin oxidoreductase free and in complex with pyruvate
-
DOI 10.1038/5870
-
Chabriere E, Charon MH, Volbeda A, Pieulle L, Hatchikian EC, Fontecilla-Camps JC (1999) Crystal structures of the key anaerobic enzyme pyruvate: ferredoxin oxidoreductase, free and in complex with pyruvate. Nat Struct Biol 6:182-190 (Pubitemid 29069782)
-
(1999)
Nature Structural Biology
, vol.6
, Issue.2
, pp. 182-190
-
-
Chabriere, E.1
Charon, M.-H.2
Volbeda, A.3
Pieulle, L.4
Hatchikian, E.C.5
Fontecilla-Camps, J.-C.6
-
46
-
-
33750124980
-
Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes
-
DOI 10.1021/jm051256o
-
Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR, Halgren TA, Sanschagrin PC, Mainz DT (2006) Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem 49:6177-6196 (Pubitemid 44595196)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.21
, pp. 6177-6196
-
-
Friesner, R.A.1
Murphy, R.B.2
Repasky, M.P.3
Frye, L.L.4
Greenwood, J.R.5
Halgren, T.A.6
Sanschagrin, P.C.7
Mainz, D.T.8
-
47
-
-
79955934260
-
-
QSite (2001) Schrodinger Inc, Portland
-
QSite (2001) Schrodinger Inc, Portland
-
-
-
-
48
-
-
79955929670
-
Jaguar 5.5
-
Bachrach SM (2004) Jaguar 5.5. J Am Chem Soc 126:5018-5028
-
(2004)
J Am Chem Soc
, vol.126
, pp. 5018-5028
-
-
Bachrach, S.M.1
-
49
-
-
79955937260
-
-
IMPACT Schrodinger Inc Portland, OR
-
IMPACT Schrodinger Inc Portland, OR
-
-
-
-
50
-
-
33947413978
-
Intermediates in dioxygen activation by methane monooxygenase: A QM/MM study
-
DOI 10.1021/ja0654074
-
Rinaldo D, Philipp DM, Lippard SJ, Friesner RA (2007) Intermediates in dioxygen activation by methane monooxygenase: a QM/MM Study. J Am Chem Soc 129:3135-3147 (Pubitemid 46449345)
-
(2007)
Journal of the American Chemical Society
, vol.129
, Issue.11
, pp. 3135-3147
-
-
Rinaldo, D.1
Philipp, D.M.2
Lippard, S.J.3
Friesner, R.A.4
-
52
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
DOI 10.1021/ja9621760, PII S0002786396021762
-
Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225-11236 (Pubitemid 26399746)
-
(1996)
Journal of the American Chemical Society
, vol.118
, Issue.45
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
53
-
-
0000189651
-
Density-functional thermochemistry 3. The role of exact exchange
-
Becke AD (1993) Density-functional thermochemistry 3. The role of exact exchange. J Chem Phys 98:5648-5652
-
(1993)
J Chem Phys
, vol.98
, pp. 5648-5652
-
-
Becke, A.D.1
-
54
-
-
4243553426
-
Density-functional exchange-energy approximation with correct asymptotic-behavior
-
Becke AD (1988) Density-functional exchange-energy approximation with correct asymptotic-behavior. Phys Rev A 38: 3098-3100
-
(1988)
Phys Rev A
, vol.38
, pp. 3098-3100
-
-
Becke, A.D.1
-
55
-
-
0345491105
-
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron-density
-
Lee CT, Yang WT, Parr RG (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron-density. Phys Rev B 37:785-789
-
(1988)
Phys Rev B
, vol.37
, pp. 785-789
-
-
Lee, C.T.1
Yang, W.T.2
Parr, R.G.3
-
56
-
-
1242346134
-
-
Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ Gaussian03
-
Gaussian03
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
Cheeseman, J.R.6
Scalmani, G.7
Barone, V.8
Mennucci, B.9
Petersson, G.A.10
Nakatsuji, H.11
Caricato, M.12
Li, X.13
Hratchian, H.P.14
Izmaylov, A.F.15
Bloino, J.16
Zheng, G.17
Sonnenberg, J.L.18
Hada, M.19
Ehara, M.20
Toyota, K.21
Fukuda, R.22
Hasegawa, J.23
Ishida, M.24
Nakajima, T.25
Honda, Y.26
Kitao, O.27
Nakai, H.28
Vreven, T.29
Montgomery Jr., J.A.30
Peralta, J.E.31
Ogliaro, F.32
Bearpark, M.33
Heyd, J.J.34
Brothers, E.35
Kudin, K.N.36
Staroverov, V.N.37
Kobayashi, R.38
Normand, J.39
Raghavachari, K.40
Rendell, A.41
Burant, J.C.42
Iyengar, S.S.43
Tomasi, J.44
Cossi, M.45
Rega, N.46
Millam, J.M.47
Klene, M.48
Knox, J.E.49
Cross, J.B.50
Bakken, V.51
Adamo, C.52
Jaramillo, J.53
Gomperts, R.54
Stratmann, R.E.55
Yazyev, O.56
Austin, A.J.57
Cammi, R.58
Pomelli, C.59
Ochterski, J.W.60
Martin, R.L.61
Morokuma, K.62
Zakrzewski, V.G.63
Voth, G.A.64
Salvador, P.65
Dannenberg, J.J.66
Dapprich, S.67
Daniels, A.D.68
Farkas, Ö.69
Foresman, J.B.70
Ortiz, J.V.71
Cioslowski, J.72
Fox, D.J.73
more..
-
57
-
-
84962361532
-
Benchmarking the conductor-like polarizable
-
continuum model (CPCM) for aqueous solvation free energies of neutral and ionic organic molecules.
-
Takano Y, Houk KN (2005) Benchmarking the conductor-like polarizable continuum model (CPCM) for aqueous solvation free energies of neutral and ionic organic molecules. J Chem Theory Comput 1:70-77
-
(2005)
J Chem Theory Comput
, vol.1
, pp. 70-77
-
-
Takano, Y.1
Houk, K.N.2
-
58
-
-
84962349001
-
Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model
-
Cossi M, Rega N, Scalmani G, Barone V (2003) Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model. J Comput Chem 24:669-681
-
(2003)
J Comput Chem
, vol.24
, pp. 669-681
-
-
Cossi, M.1
Rega, N.2
Scalmani, G.3
Barone, V.4
-
59
-
-
84961985847
-
Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model
-
Barone V, Cossi M (1998) Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. J Phys Chem A 102:1995-2001 (Pubitemid 128591338)
-
(1998)
Journal of Physical Chemistry A
, vol.102
, Issue.11
, pp. 1995-2001
-
-
Barone, V.1
Cossi, M.2
-
60
-
-
0037898938
-
Pyruvate ferredoxin oxidoreductase and its radical intermediate
-
Ragsdale SW (2003) Pyruvate ferredoxin oxidoreductase and its radical intermediate. Chem Rev 103:2333-2346
-
(2003)
Chem Rev
, vol.103
, pp. 2333-2346
-
-
Ragsdale, S.W.1
-
61
-
-
26844525476
-
Theoretical study toward understanding the catalytic mechanism of pyruvate decarboxylase
-
DOI 10.1021/jp052802s
-
Wang JY, Dong H, Li SH, He HW (2005) Theoretical study toward understanding the catalytic mechanism of pyruvate decarboxylase. J Phys Chem B 109:18664-18672 (Pubitemid 41464201)
-
(2005)
Journal of Physical Chemistry B
, vol.109
, Issue.39
, pp. 18664-18672
-
-
Wang, J.1
Dong, H.2
Li, S.3
He, H.4
-
62
-
-
67649476220
-
Recent developments of the quantum chemical cluster approach for modeling enzyme reactions
-
Siegbahn P, Himo F (2009) Recent developments of the quantum chemical cluster approach for modeling enzyme reactions. J Biol Inorg Chem 14:643-651
-
(2009)
J Biol Inorg Chem
, vol.14
, pp. 643-651
-
-
Siegbahn, P.1
Himo, F.2
-
63
-
-
67650549945
-
S K-edge XAS and DFT calculations on cytochrome P450: Covalent and ionic contributions to the cysteine-Fe bond and their contribution to reactivity
-
Dey A, Jiang Y, Ortiz de Montellano P, Hodgson KO, Hedman B, Solomon EI (2009) S K-edge XAS and DFT calculations on cytochrome P450: covalent and ionic contributions to the cysteine-Fe bond and their contribution to reactivity. J Am Chem Soc 131:7869-7878
-
(2009)
J Am Chem Soc
, vol.131
, pp. 7869-7878
-
-
Dey, A.1
Jiang, Y.2
Ortiz De Montellano, P.3
Hodgson, K.O.4
Hedman, B.5
Solomon, E.I.6
-
64
-
-
84962476358
-
Solvent effects on electronic structure of active site of azurin by polarizable continuum model
-
Sugimori K, Shuku T, Sugiyama A, Nagao H, Sakurai T, Nishikawa K (2005) Solvent effects on electronic structure of active site of azurin by polarizable continuum model. Polyhedron 24:2671-2675
-
(2005)
Polyhedron
, vol.24
, pp. 2671-2675
-
-
Sugimori, K.1
Shuku, T.2
Sugiyama, A.3
Nagao, H.4
Sakurai, T.5
Nishikawa, K.6
-
65
-
-
0035930716
-
Crystal structure of the free radical intermediate of pyruvate:ferredoxin oxidoreductase
-
DOI 10.1126/science.1066198
-
Chabriere E, Vernede C, Guigliarelli B, Charon MH, Hatchikian EC, Fontecilla-Camps JC (2001) Crystal structure of the free radical intermediate of pyruvate: ferredoxin oxidoreductase. Science 294:2559-2563 (Pubitemid 34027298)
-
(2001)
Science
, vol.294
, Issue.5551
, pp. 2559-2563
-
-
Chabriere, E.1
Vernede, X.2
Guigliarelli, B.3
Charon, M.-H.4
Hatchikian, E.C.5
Fontecilla-Camps, J.C.6
-
66
-
-
0032784415
-
Structure and electron transfer mechanism of pyruvate: Ferredoxin oxidoreductase
-
Charon MH, Volbeda A, Chabriere E, Pieulle L, Fontecilla- Camps JC (1999) Structure and electron transfer mechanism of pyruvate: ferredoxin oxidoreductase. Curr Opin Struct Biol 9:663-669
-
(1999)
Curr Opin Struct Biol
, vol.9
, pp. 663-669
-
-
Charon, M.H.1
Volbeda, A.2
Chabriere, E.3
Pieulle, L.4
Fontecilla-Camps, J.C.5
-
67
-
-
0034609527
-
Mechanism of elementary catalytic steps of pyruvate oxidase from Lactobacillus plantarum
-
Tittmann K, Golbik R, Ghisla S, Hubner G (2000) Mechanism of elementary catalytic steps of pyruvate oxidase from Lactobacillus plantarum. Biochemistry 39:10747-10754
-
(2000)
Biochemistry
, vol.39
, pp. 10747-10754
-
-
Tittmann, K.1
Golbik, R.2
Ghisla, S.3
Hubner, G.4
-
68
-
-
47349102781
-
Thiamin diphosphate catalysis: Enzymic and nonenzymic covalent intermediates
-
Kluger R, Tittmann K (2008) Thiamin diphosphate catalysis: enzymic and nonenzymic covalent intermediates. Chem Rev 108:1797-1833
-
(2008)
Chem Rev
, vol.108
, pp. 1797-1833
-
-
Kluger, R.1
Tittmann, K.2
-
69
-
-
0034666137
-
The role of pyruvate ferredoxin oxidoreductase in pyruvate synthesis during autotrophic growth by the Wood-Ljungdahl pathway
-
Furdui C, Ragsdale SW (2000) The role of pyruvate ferredoxin oxidoreductase in pyruvate synthesis during autotrophic growth by the Wood-Ljungdahl pathway. J Biol Chem 275:28494-28499
-
(2000)
J Biol Chem
, vol.275
, pp. 28494-28499
-
-
Furdui, C.1
Ragsdale, S.W.2
-
70
-
-
0031013992
-
How thiamine diphosphate is activated in enzymes
-
DOI 10.1126/science.275.5296.67
-
Kern D, Kern G, Neef H, Tittmann K, KillenbergJabs M, Wikner C, Schneider G, Hubner G (1997) How thiamine diphosphate is activated in enzymes. Science 275:67-70 (Pubitemid 27020308)
-
(1997)
Science
, vol.275
, Issue.5296
, pp. 67-70
-
-
Kern, D.1
Kern, G.2
Neef, H.3
Tittmann, K.4
Killenberg-Jabs, M.5
Wikner, C.6
Schneider, G.7
Hubner, G.8
-
71
-
-
0142135980
-
Dual Catalytic Apparatus of the Thiamin Diphosphate Coenzyme: Acid-Base via the 1′,4′-Iminopyrimidine Tautomer along with Its Electrophilic Role
-
DOI 10.1021/ja0346126
-
Jordan F, Nemeria NS, Zhang S, Yan Y, Arjunan P, Furey W (2003) Dual catalytic apparatus of the thiamin diphosphate coenzyme: acid-base via the 1′, 4′-iminopyrimidine tautomer along with its electrophilic role. J Am Chem Soc 125:12732-12738 (Pubitemid 37280442)
-
(2003)
Journal of the American Chemical Society
, vol.125
, Issue.42
, pp. 12732-12738
-
-
Jordan, F.1
Nemeria, N.S.2
Zhang, S.3
Yan, Y.4
Arjunan, P.5
Furey, W.6
-
72
-
-
0032537475
-
Theoretical studies on the electronic and energetic properties of the aminopyrimidine part of thiamin diphosphate
-
DOI 10.1016/S0167-4838(98)00072-7, PII S0167483898000727
-
Friedemann R, Neef H (1998) Theoretical studies on the electronic and energetic properties of the aminopyrimidine part of thiamin diphosphate. Biochim Biophys Acta Protein Struct Mol Enzymol 1385:245-250 (Pubitemid 28310792)
-
(1998)
Biochimica et Biophysica Acta - Protein Structure and Molecular Enzymology
, vol.1385
, Issue.2
, pp. 245-250
-
-
Friedemann, R.1
Neef, H.2
-
73
-
-
0027366618
-
Decomposition of 2-(1-hydroxybenzyl)thiamin in neutral aqueous solutions: Benzaldehyde and thiamin are not the products
-
DOI 10.1006/bioo.1993.1023
-
Kluger R, Lam JF, Kim CS (1993) Decomposition of 2- (1-hydroxybenzyl) thiamin in neutral aqueous-solutions - benzaldehyde and thiamin are not the products. Bioorg Chem 21:275-283 (Pubitemid 23285425)
-
(1993)
Bioorganic Chemistry
, vol.21
, Issue.3
, pp. 275-283
-
-
Kluger, R.1
Lam, J.F.2
Kim, C.-S.3
-
74
-
-
0023719226
-
Thiamin diphosphate catalysis - Mechanistic divergence as a probe of substrate activation of pyruvate decarboxylase
-
Gish G, Smyth T, Kluger R (1988) Thiamin diphosphate catalysis - mechanistic divergence as a probe of substrate activation of pyruvate decarboxylase. J Am Chem Soc 110:6230-6234
-
(1988)
J Am Chem Soc
, vol.110
, pp. 6230-6234
-
-
Gish, G.1
Smyth, T.2
Kluger, R.3
-
75
-
-
38049001166
-
Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels
-
Atsumi S, Hanai T, Liao JC (2008) Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451(7174):86-89
-
(2008)
Nature
, vol.451
, Issue.7174
, pp. 86-89
-
-
Atsumi, S.1
Hanai, T.2
Liao, J.C.3
-
77
-
-
27844505722
-
Advances in protein structure prediction and de novo protein design: A review
-
Floudas CA, Fung HK, McAllister SR, Monnigmann M, Rajgaria R (2005) Advances in protein structure prediction and de novo protein design: a review. Chem Eng Sci 61:966-988
-
(2005)
Chem Eng Sci
, vol.61
, pp. 966-988
-
-
Floudas, C.A.1
Fung, H.K.2
McAllister, S.R.3
Monnigmann, M.4
Rajgaria, R.5
|