-
1
-
-
0030369489
-
Glutamate and 2-methyleneglutarate mutase: From microbial curiosities to paradigms for coenzyme B12-dependent enzymes
-
Buckel W, Golding BT. Glutamate and 2-methyleneglutarate mutase: from microbial curiosities to paradigms for coenzyme B12-dependent enzymes. Chem Soc Rev 1996;25:329-338.
-
(1996)
Chem Soc Rev
, vol.25
, pp. 329-338
-
-
Buckel, W.1
Golding, B.T.2
-
3
-
-
21844449665
-
Chemistry and enzymology of vitamin B12
-
Brown K. Chemistry and Enzymology of Vitamin B12. Chem Rev 2005;105:2075-2149.
-
(2005)
Chem Rev
, vol.105
, pp. 2075-2149
-
-
Brown, K.1
-
4
-
-
0037560995
-
Radical catalysis in coenzyme B12-dependent isomerization (eliminating) reactions
-
Toraya T. Radical Catalysis in Coenzyme B12-Dependent Isomerization (Eliminating) Reactions. Chem Rev 2003;103:2095-2127.
-
(2003)
Chem Rev
, vol.103
, pp. 2095-2127
-
-
Toraya, T.1
-
7
-
-
0032023777
-
Protein radicals in enzyme catalysis
-
Stubbe J, van der Donk W. Protein radicals in enzyme catalysis. Chem Rev 1998;98:705-762.
-
(1998)
Chem Rev
, vol.98
, pp. 705-762
-
-
Stubbe, J.1
Van Der Donk, W.2
-
8
-
-
84855620601
-
-
Dolphin D, editor. New York: Wiley
-
Dolphin D, editor. B12. Volume 1. New York: Wiley; 1982.
-
(1982)
B12
, vol.1
-
-
-
9
-
-
0029294618
-
A radical approach to enzyme catalysis
-
Marsh ENG. A radical approach to enzyme catalysis. Bioessays 1995;17:431-441.
-
(1995)
Bioessays
, vol.17
, pp. 431-441
-
-
Marsh, E.N.G.1
-
10
-
-
0035478124
-
Adenosylcobalamin-dependent isomerases: New insights into structure and mechanism
-
Marsh ENG, Drennan CL. Adenosylcobalamin-dependent isomerases: new insights into structure and mechanism. Current Opinion in Chemical Biology 2001;5:499-505.
-
(2001)
Current Opinion in Chemical Biology
, vol.5
, pp. 499-505
-
-
Marsh, E.N.G.1
Drennan, C.L.2
-
11
-
-
0030584657
-
How coenzyme B12 radicals are generated: The crystal structure of methylmalonylcoenzyme a mutase at 2 a resolution
-
Mancia F, Keep NH, Nakagawa A, Leadlay PF, McSweeney S, Rasmussen B, Bösecke P, Diat O, Evans PR. How coenzyme B12 radicals are generated: the crystal structure of methylmalonylcoenzyme A mutase at 2 A resolution. Structure 1996;4:339-350.
-
(1996)
Structure
, vol.4
, pp. 339-350
-
-
Mancia, F.1
Keep, N.H.2
Nakagawa, A.3
Leadlay, P.F.4
McSweeney, S.5
Rasmussen, B.6
Bösecke, P.7
Diat, O.8
Evans, P.R.9
-
12
-
-
0032526407
-
Conformational changes on substrate binding to methylmalonyl-CoA mutase and new insights into the free radical mechanism
-
Mancia F, Evans PR. Conformational changes on substrate binding to methylmalonyl-CoA mutase and new insights into the free radical mechanism. Structure 1998;6:711-720.
-
(1998)
Structure
, vol.6
, pp. 711-720
-
-
Mancia, F.1
Evans, P.R.2
-
13
-
-
0033594923
-
Crystal structure of substrate complexes of methylmalonyl-CoA mutase
-
Mancia F, Smith GA, Evans PR. Crystal structure of substrate complexes of methylmalonyl-CoA mutase. Biochemistry 1999;38:7999-8005.
-
(1999)
Biochemistry
, vol.38
, pp. 7999-8005
-
-
Mancia, F.1
Smith, G.A.2
Evans, P.R.3
-
14
-
-
0033566661
-
Glutamate mutase from Clostridium cochlearium: The structure of a coenzyme B12-dependent enzyme provides new mechanistic insights
-
Reitzer R, Gruber K, Jogl G, Wagner UG, Bothe H, Buckel W, Kratky C. Glutamate mutase from Clostridium cochlearium: the structure of a coenzyme B12-dependent enzyme provides new mechanistic insights. Structure 1999;7:891-902.
-
(1999)
Structure
, vol.7
, pp. 891-902
-
-
Reitzer, R.1
Gruber, K.2
Jogl, G.3
Wagner, U.G.4
Bothe, H.5
Buckel, W.6
Kratky, C.7
-
16
-
-
0033567082
-
A new mode of B12 binding and the direct participation of a potassium ion in enyzme catalysis: X-ray structure of diol dehydratase
-
Shibata N, Masuda J, Tobimatsu T, Toraya T, Suto K, Morimoto Y, Yasuoka N. A new mode of B12 binding and the direct participation of a potassium ion in enyzme catalysis: X-ray structure of diol dehydratase. Structure 1999;7:997-1008.
-
(1999)
Structure
, vol.7
, pp. 997-1008
-
-
Shibata, N.1
Masuda, J.2
Tobimatsu, T.3
Toraya, T.4
Suto, K.5
Morimoto, Y.6
Yasuoka, N.7
-
17
-
-
0034661847
-
How a protein generates a catalytic radical from coenzyme B12: X-ray structure of a diol dehydratase-adeninylpentylcobalamin complex
-
Masuda J, Shibata N, Morimoto Y, Toraya T, Yasuoka N. How a protein generates a catalytic radical from coenzyme B12: X-ray structure of a diol dehydratase-adeninylpentylcobalamin complex. Structure 2000;8:775-788.
-
(2000)
Structure
, vol.8
, pp. 775-788
-
-
Masuda, J.1
Shibata, N.2
Morimoto, Y.3
Toraya, T.4
Yasuoka, N.5
-
18
-
-
18544379948
-
12-dependent glycerol dehydratase in complex with cobalamin and propane-1,2-diol
-
12-Dependent Glycerol Dehydratase in Complex with Cobalamin and Propane-1,2-Diol. Eur J Biochem 2002;269:4484-4494.
-
(2002)
Eur J Biochem
, vol.269
, pp. 4484-4494
-
-
Yaminishi, M.1
Yunoki, M.2
Tobimatsu, T.3
Sato, H.4
Matsui, J.5
Dokiya, A.6
Iuchi, Y.7
Oe, K.8
Suto, K.9
Shibata, N.10
Morimoto, Y.11
Yasuoka, N.12
Toraya, T.13
-
19
-
-
0037245309
-
Crystal structure of substrate free form of glycerol dehydratase
-
Liao D-I, Dotson G, Turner I, Reiss L, Emptage M. Crystal Structure of Substrate Free Form of Glycerol Dehydratase. J Inorg Biochem 2003;93:84-91.
-
(2003)
J Inorg Biochem
, vol.93
, pp. 84-91
-
-
Liao, D.-I.1
Dotson, G.2
Turner, I.3
Reiss, L.4
Emptage, M.5
-
20
-
-
0036219377
-
The crystal structure of class II ribonucleotide reductase reveals how an allosterically regulated monomer mimics a dimer
-
Sintchak MD, Arjara G, Kellogg BA, Stubbe J, Drennan CL. The Crystal Structure of Class II Ribonucleotide Reductase Reveals How an Allosterically Regulated Monomer Mimics a Dimer. Nature Struct Biol 2002;9:293-300.
-
(2002)
Nature Struct Biol
, vol.9
, pp. 293-300
-
-
Sintchak, M.D.1
Arjara, G.2
Kellogg, B.A.3
Stubbe, J.4
Drennan, C.L.5
-
22
-
-
3242882336
-
AdoMet radical proteins-from structure to evolution-alignment of divergent protein sequences reveals strong secondary structure element conservation
-
Nicolet Y, Drennan CL. AdoMet radical proteins-from structure to evolution-alignment of divergent protein sequences reveals strong secondary structure element conservation. Nucleic Acids Res 2004;32(13):4015-4025.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.13
, pp. 4015-4025
-
-
Nicolet, Y.1
Drennan, C.L.2
-
23
-
-
0035282866
-
Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: Functional characterization using new analysis and information visualization methods
-
Sophia HJ, Chen G, Hetzler BG, Reyes-Spindola JF, Miller NE. Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. Nucleic Acids Res 2001;29:1097-1106.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 1097-1106
-
-
Sophia, H.J.1
Chen, G.2
Hetzler, B.G.3
Reyes-Spindola, J.F.4
Miller, N.E.5
-
24
-
-
0034912671
-
Radical mechanisms of enzymatic catalysis
-
Frey P. Radical mechanisms of enzymatic catalysis. Ann Rev Biochem 2001;70:121-148.
-
(2001)
Ann Rev Biochem
, vol.70
, pp. 121-148
-
-
Frey, P.1
-
25
-
-
0037399004
-
The generation of 5′-deoxyadenosyl radicals by adenosylmethionine- dependent radical enzymes
-
Jarrett JT. The generation of 5′-deoxyadenosyl radicals by adenosylmethionine-dependent radical enzymes. Curr Opin Chem Biol 2003;7:174-182.
-
(2003)
Curr Opin Chem Biol
, vol.7
, pp. 174-182
-
-
Jarrett, J.T.1
-
26
-
-
0035830318
-
5-Deoxyadenosine contacts the substrate radical intermediate in the active site of ethanolamine ammonia-lyase: 2H and 13C electron nuclear double resonance studies
-
Lobrutto R, Bandarian V, Magnusson OT, Chen X, Schramm VL, Reed GH. 5-Deoxyadenosine Contacts the Substrate Radical Intermediate in the Active Site of Ethanolamine Ammonia-Lyase: 2H and 13C Electron Nuclear Double Resonance Studies. Biochemistry 2001;40:9-14.
-
(2001)
Biochemistry
, vol.40
, pp. 9-14
-
-
Lobrutto, R.1
Bandarian, V.2
Magnusson, O.T.3
Chen, X.4
Schramm, V.L.5
Reed, G.H.6
-
27
-
-
0035812388
-
Interaction of the substrate radical and the 5′-deoxyadenosine- 5′-methyl group in vitamin B12 coenzyme-dependent ethanolamine deaminase
-
Warncke K, Utada AS. Interaction of the Substrate Radical and the 5′-Deoxyadenosine-5′-Methyl Group in Vitamin B12 Coenzyme-Dependent Ethanolamine Deaminase. J Am Chem Soc 2001;123:8564-8572.
-
(2001)
J Am Chem Soc
, vol.123
, pp. 8564-8572
-
-
Warncke, K.1
Utada, A.S.2
-
28
-
-
0037194941
-
Geometry of reactant centers in the coil-substrate radical pair state of coenzyme B12-dependent ethanolamine deaminase determined by using orientation-selection-ESEEM spectroscopy
-
Canfield JM, Warncke K. Geometry of Reactant Centers in the Coil-Substrate Radical Pair State of Coenzyme B12-Dependent Ethanolamine Deaminase Determined by using Orientation-Selection-ESEEM Spectroscopy. J Phys Chem B 2002;106:8831-8841.
-
(2002)
J Phys Chem B
, vol.106
, pp. 8831-8841
-
-
Canfield, J.M.1
Warncke, K.2
-
29
-
-
0037047017
-
Analysis of the electron paramagnetic resonance spectrum of a radical intermediate in the coenyzme B12-dependent ethanolamine ammonia-lyase catalyzed reaction of S-2-aminopropanol
-
Bandarian V, Reed GH. Analysis of the Electron Paramagnetic Resonance Spectrum of a Radical Intermediate in the Coenyzme B12-Dependent Ethanolamine Ammonia-Lyase Catalyzed Reaction of S-2-Aminopropanol. Biochemistry 2002;41:8580-8588.
-
(2002)
Biochemistry
, vol.41
, pp. 8580-8588
-
-
Bandarian, V.1
Reed, G.H.2
-
30
-
-
14644444206
-
Characterization of the product radical structure in the coil-product radical pair state of coenzyme B12-dependent ethanolamine deaminase by using three-pulse 2H ESEEM spectroscopy
-
Warncke K. Characterization of the Product Radical Structure in the Coil-Product Radical Pair State of Coenzyme B12-Dependent Ethanolamine Deaminase by using Three-Pulse 2H ESEEM Spectroscopy. Biochemistry 2005;44:3184-3193.
-
(2005)
Biochemistry
, vol.44
, pp. 3184-3193
-
-
Warncke, K.1
-
31
-
-
14544273647
-
Active site reactant center geometry in the coil-product radical pair state of coenzyme B12-dependent ethanolamine deaminase determined by using orientation-selection-ESEEM spectroscopy
-
Canfield JM, Warncke K. Active Site Reactant Center Geometry in the Coil-Product Radical Pair State of Coenzyme B12-Dependent Ethanolamine Deaminase Determined by Using Orientation-Selection-ESEEM Spectroscopy. J Phys Chem B 2005;109:3053-3046.
-
(2005)
J Phys Chem B
, vol.109
, pp. 3053-13046
-
-
Canfield, J.M.1
Warncke, K.2
-
32
-
-
0001916849
-
Ethanolamine ammonia-lyase
-
Banerjee R, editor. New York: John Wiley and Sons
-
Bandarian V, Reed GH. Ethanolamine Ammonia-Lyase. In: Banerjee R, editor. Chemistry and Biochemistry of B12. New York: John Wiley and Sons; 1999. p 811-833.
-
(1999)
Chemistry and Biochemistry of B12
, pp. 811-833
-
-
Bandarian, V.1
Reed, G.H.2
-
33
-
-
0013832936
-
The clostridial fermentations of choline and ethanolamine
-
Bradbeer C. The Clostridial Fermentations of Choline and Ethanolamine. J Biol Chem 1965;240:4669.
-
(1965)
J Biol Chem
, vol.240
, pp. 4669
-
-
Bradbeer, C.1
-
34
-
-
0037205888
-
Computational exploration of rearrangements related to the vitamin B12-dependent ethanolamine ammonia lyase catalyzed transformation
-
Samialjac M, Schwartz H. Computational exploration of rearrangements related to the vitamin B12-dependent ethanolamine ammonia lyase catalyzed transformation. J Am Chem Soc 2002;124:8974-8983.
-
(2002)
J Am Chem Soc
, vol.124
, pp. 8974-8983
-
-
Samialjac, M.1
Schwartz, H.2
-
35
-
-
0037184475
-
Understanding the mechanism of action of B12-dependent ethanolamine ammonia-lyase: Synergistic interactions at play
-
Wetmore SD, Smith DM, Bennet JT, Radom L. Understanding the Mechanism of Action of B12-Dependent Ethanolamine Ammonia-Lyase: Synergistic Interactions at Play. J Am Chem Soc 2002;124:14054-14065.
-
(2002)
J Am Chem Soc
, vol.124
, pp. 14054-14065
-
-
Wetmore, S.D.1
Smith, D.M.2
Bennet, J.T.3
Radom, L.4
-
36
-
-
0042338528
-
Computational study on mechanistic details, of the aminoethanol rearrangement catalyzed by the vitamin B12-dependent ethanolamine ammonia lyase: His and Asp/Glu acting simultaneously as catalytic auxiliaries
-
Samialjac M, Schwartz H. Computational study on mechanistic details, of the aminoethanol rearrangement catalyzed by the vitamin B12-dependent ethanolamine ammonia lyase: His and Asp/Glu acting simultaneously as catalytic auxiliaries. J Org Chem 2003;68:6967-6983.
-
(2003)
J Org Chem
, vol.68
, pp. 6967-6983
-
-
Samialjac, M.1
Schwartz, H.2
-
37
-
-
20944437413
-
Divergent mechanisms of suicide inactivation for ethanolamine ammonia-lyase
-
Sandala GM, Smith DM, Radom L. Divergent mechanisms of suicide inactivation for ethanolamine ammonia-lyase. J Am Chem Soc 2005;127:8856-8864.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 8856-8864
-
-
Sandala, G.M.1
Smith, D.M.2
Radom, L.3
-
38
-
-
3042536077
-
Computational investigation of hydrogen abstraction from 2-aminoethanol by the 1,5-dideoxy-5-yl radical: A model study of a reaction occurring in the active site of ethanolamine ammonia lyase
-
Samialjac M, Schwartz H. Computational investigation of hydrogen abstraction from 2-aminoethanol by the 1,5-dideoxy-5-yl radical: A model study of a reaction occurring in the active site of ethanolamine ammonia lyase. Chem Eur J 2004;10:2781-2788.
-
(2004)
Chem Eur J
, vol.10
, pp. 2781-2788
-
-
Samialjac, M.1
Schwartz, H.2
-
39
-
-
0035961591
-
Understanding the mechanism of B12-dependent diol dehydratase: A synergistic retro-push-pull proposal
-
Smith DM, Golding BT, Radom L. Understanding the mechanism of B12-dependent diol dehydratase: A synergistic retro-push-pull proposal. J Am Chem Soc 2001;123:1664-1675.
-
(2001)
J Am Chem Soc
, vol.123
, pp. 1664-1675
-
-
Smith, D.M.1
Golding, B.T.2
Radom, L.3
-
40
-
-
10344257551
-
Catalytic roles of active-site amino acid residues of coenzyme B12-dependent diol dehydratase: Protonation state of histidine and pull effect of glutamate
-
Kamachi T, Toraya T, Yoshizawa K. Catalytic Roles of Active-Site Amino Acid Residues of Coenzyme B12-Dependent Diol Dehydratase: Protonation State of Histidine and Pull Effect of Glutamate. J Am Chem Soc 2004;126:16207-16216.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 16207-16216
-
-
Kamachi, T.1
Toraya, T.2
Yoshizawa, K.3
-
41
-
-
0026572107
-
Overexpression, purification and some properties of AdoCbl-dependent ethanolamine amino-lyase from Salmonella typhimurium
-
Faust LP, Babior BM. Overexpression, purification and some properties of AdoCbl-dependent ethanolamine amino-lyase from Salmonella typhimurium. Arch Biochem Biophys 1992;294:50-54.
-
(1992)
Arch Biochem Biophys
, vol.294
, pp. 50-54
-
-
Faust, L.P.1
Babior, B.M.2
-
42
-
-
0019071337
-
The number of functional sites per molecule of the adenosylcobalamin- dependent enzyme, ethanolamine deaminase, as determined by a kinetic method
-
Hollaway MR, Johnson AW, Lappert MF, Wallis OC. The number of functional sites per molecule of the adenosylcobalamin-dependent enzyme, ethanolamine deaminase, as determined by a kinetic method. Eur J Biochem 1980;111:177-188.
-
(1980)
Eur J Biochem
, vol.111
, pp. 177-188
-
-
Hollaway, M.R.1
Johnson, A.W.2
Lappert, M.F.3
Wallis, O.C.4
-
43
-
-
0033592455
-
Hydrazine cation radical in the active site of ethanolamine ammonia-lyase: Mechanism-based inactivation by hydroxyethylhydrazine
-
Bandarian V, Reed GH. Hydrazine cation radical in the active site of ethanolamine ammonia-lyase: mechanism-based inactivation by hydroxyethylhydrazine. Biochemistry 1999;38:12394-12402.
-
(1999)
Biochemistry
, vol.38
, pp. 12394-12402
-
-
Bandarian, V.1
Reed, G.H.2
-
44
-
-
0036129154
-
Structural genomics: A pipeline for providing structures for the biologist
-
Chance MR, al. e. Structural genomics: A pipeline for providing structures for the biologist. Prot Sci 2002;11:723-738.
-
(2002)
Prot Sci
, vol.11
, pp. 723-738
-
-
Chance, M.R.1
-
45
-
-
0025286022
-
AdoCbl-dependent ethanolamine amino-lyase from Salmonella typhimurium
-
Faust LP, Connor JA, Roof DM, Hoch JA, Babior BM. AdoCbl-dependent ethanolamine amino-lyase from Salmonella typhimurium. J Biol Chem 1990;265:12462-12466.
-
(1990)
J Biol Chem
, vol.265
, pp. 12462-12466
-
-
Faust, L.P.1
Connor, J.A.2
Roof, D.M.3
Hoch, J.A.4
Babior, B.M.5
-
46
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altscul SF, Madden TL, Schaeffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altscul, S.F.1
Madden, T.L.2
Schaeffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
47
-
-
0033873929
-
Comparative protein structure modelling of genes and genomes
-
Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A. Comparative protein structure modelling of genes and genomes. Annual Review of Biophysics and Biomolecular Structure 2000;29:291-325.
-
(2000)
Annual Review of Biophysics and Biomolecular Structure
, vol.29
, pp. 291-325
-
-
Marti-Renom, M.A.1
Stuart, A.C.2
Fiser, A.3
Sanchez, R.4
Melo, F.5
Sali, A.6
-
48
-
-
0027136282
-
Comparative modelling by satisfaction of spatial constraints
-
Sali A, Blundell TL. Comparative modelling by satisfaction of spatial constraints. J Mol Biol 1993;234:779-815.
-
(1993)
J Mol Biol
, vol.234
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
49
-
-
33745616750
-
-
Enzyme database - BRENDA url: http://www.brenda.uni-koeln.de/. Volume 2004; 1987.
-
(1987)
Enzyme Database - BRENDA
, vol.2004
-
-
-
50
-
-
0037255072
-
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
-
Boeckmann B, Bairoch A, Blatter M-C, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003;31:354-370.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 354-370
-
-
Boeckmann, B.1
Bairoch, A.2
Blatter, M.-C.3
Estreicher, A.4
Gasteiger, E.5
Martin, M.J.6
Michoud, K.7
O'Donovan, C.8
Phan, I.9
Pilbout, S.10
Schneider, M.11
-
51
-
-
0043123216
-
GeneSilico protein structure prediction meta-server
-
Kurowski MA, Bujnicki JM. GeneSilico Protein Structure Prediction Meta-Server. Nucleic Acids Res 2003;31(13):3305-3307.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3305-3307
-
-
Kurowski, M.A.1
Bujnicki, J.M.2
-
52
-
-
0034595501
-
Enhanced genome annotation using structural profiles in the program 3D-PSSM
-
Kelley LA, McCallum CM, Sternberg MJ. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol 2000;299:501-522.
-
(2000)
J Mol Biol
, vol.299
, pp. 501-522
-
-
Kelley, L.A.1
McCallum, C.M.2
Sternberg, M.J.3
-
53
-
-
0033997036
-
Comparison of sequence profiles. Strategies for structural predictions using sequence information
-
Rychlewski L, Jaroszewski L, Li W, Godzik A. Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci 2000;9:232-241.
-
(2000)
Protein Sci
, vol.9
, pp. 232-241
-
-
Rychlewski, L.1
Jaroszewski, L.2
Li, W.3
Godzik, A.4
-
54
-
-
0035967880
-
Fugue: Sequence-structure homology recognition using environmnent- specific substitution tables and structure-dependent gap penalties
-
Shi J, Blundell TL, Mizuguchi K. Fugue: Sequence-structure homology recognition using environmnent-specific substitution tables and structure-dependent gap penalties. J Mol Biol 2001;310:243-257.
-
(2001)
J Mol Biol
, vol.310
, pp. 243-257
-
-
Shi, J.1
Blundell, T.L.2
Mizuguchi, K.3
-
55
-
-
0033537993
-
GenTHREADER: An efficient and reliable protein fold recognition method
-
Jones DT. GenTHREADER: An Efficient and Reliable Protein Fold Recognition Method. J Mol Biol 1999;287:797-815.
-
(1999)
J Mol Biol
, vol.287
, pp. 797-815
-
-
Jones, D.T.1
-
56
-
-
0242299169
-
Automatic consensus based fold recognition using Peons, ProQ and Pmodeller
-
Wallner B, Fang H, Elofsson A. Automatic consensus based fold recognition using Peons, ProQ and Pmodeller. Proteins 2003;53:534-541.
-
(2003)
Proteins
, vol.53
, pp. 534-541
-
-
Wallner, B.1
Fang, H.2
Elofsson, A.3
-
57
-
-
0032438987
-
Hidden Markov models for detecting remote protein homologies
-
Karplus K. Hidden Markov Models for Detecting Remote Protein Homologies. Bioinformatics 1998;14(10):846-856.
-
(1998)
Bioinformatics
, vol.14
, Issue.10
, pp. 846-856
-
-
Karplus, K.1
-
58
-
-
0242362161
-
Combining local-structure, fold-recognition, and new-fold methods for protein structure prediction
-
Karplus K, Karchin R, Barret C, Tu S, Cline M, Diekhans M, Grate L, Casper J, Hughey R. Combining local-structure, fold-recognition, and new-fold methods for protein structure prediction. Proteins 2003;53:491-496.
-
(2003)
Proteins
, vol.53
, pp. 491-496
-
-
Karplus, K.1
Karchin, R.2
Barret, C.3
Tu, S.4
Cline, M.5
Diekhans, M.6
Grate, L.7
Casper, J.8
Hughey, R.9
-
59
-
-
0042121237
-
Multiple sequence alignment with the Clustal series of programs
-
Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 2003;31(13):3497-3500.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3497-3500
-
-
Chenna, R.1
Sugawara, H.2
Koike, T.3
Lopez, R.4
Gibson, T.J.5
Higgins, D.G.6
Thompson, J.D.7
-
60
-
-
9144257886
-
The Pfam protein families database
-
Bateman A, Lachlan C, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer ELL, Studholme DJ, Yeats C, Eddy SR. The Pfam Protein Families Database. Nucleic Acids Res 2004;32:D138-D141
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Bateman, A.1
Lachlan, C.2
Durbin, R.3
Finn, R.D.4
Hollich, V.5
Griffiths-Jones, S.6
Khanna, A.7
Marshall, M.8
Moxon, S.9
Sonnhammer, E.L.L.10
Studholme, D.J.11
Yeats, C.12
Eddy, S.R.13
-
61
-
-
0025341310
-
Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
-
Sippl MJ. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 1990;213:859-88.
-
(1990)
J Mol Biol
, vol.213
, pp. 859-888
-
-
Sippl, M.J.1
-
62
-
-
0000790849
-
From secondary structure to three-dimensional structure: Improved dihedral angle probability distribution function for use with energy searches for native structures of polypeptides and proteins
-
Cheng B, Nayeem A, Scheraga HA. From secondary structure to three-dimensional structure: Improved dihedral angle probability distribution function for use with energy searches for native structures of polypeptides and proteins. J Comp Chem 1996;17:1453-1480.
-
(1996)
J Comp Chem
, vol.17
, pp. 1453-1480
-
-
Cheng, B.1
Nayeem, A.2
Scheraga, H.A.3
-
63
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD, Jr., Bashford D, Bellot M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, III, Roux M, Schlenkrich B, Smith JC, Stote J, Sträub M, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998;102:3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellot, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher III, W.E.20
Roux, M.21
Schlenkrich, B.22
Smith, J.C.23
Stote, J.24
Sträub, M.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
64
-
-
0000243829
-
PROCHECK: A program to check the stereochemical quality of protein structures
-
Laskowski RA, McArthur MW, Moss DS, Thornton JM. PROCHECK: A program to check the stereochemical quality of protein structures. J Appl Cryst 1993;26:283-291.
-
(1993)
J Appl Cryst
, vol.26
, pp. 283-291
-
-
Laskowski, R.A.1
McArthur, M.W.2
Moss, D.S.3
Thornton, J.M.4
-
65
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
Bowie JU, Luthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991;253(5016):164- 170.
-
(1991)
Science
, vol.253
, Issue.5016
, pp. 164-170
-
-
Bowie, J.U.1
Luthy, R.2
Eisenberg, D.3
-
66
-
-
0026610767
-
Assessment of protein models with three-dimensional profiles
-
Luthy R, Bowie JU, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature 1992;356(6364):83-85.
-
(1992)
Nature
, vol.356
, Issue.6364
, pp. 83-85
-
-
Luthy, R.1
Bowie, J.U.2
Eisenberg, D.3
-
67
-
-
0027490731
-
Recognition of errors in three-dimensional structures of proteins
-
Sippl MJ. Recognition of Errors in Three-Dimensional Structures of Proteins. Proteins 1993(17):355-362.
-
(1993)
Proteins
, Issue.17
, pp. 355-362
-
-
Sippl, M.J.1
-
68
-
-
0027180507
-
Verification of protein structures: Patterns of nonbonded atomic interactions
-
Colovos C, Yeates TO. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 1993;2(9):1511-1519.
-
(1993)
Protein Sci
, vol.2
, Issue.9
, pp. 1511-1519
-
-
Colovos, C.1
Yeates, T.O.2
-
69
-
-
0346727529
-
Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme
-
Berkovitch F, Nicolet Y, Wan JT, Jarret JT, Drennan CL. Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme. Science 2004;303:76-79.
-
(2004)
Science
, vol.303
, pp. 76-79
-
-
Berkovitch, F.1
Nicolet, Y.2
Wan, J.T.3
Jarret, J.T.4
Drennan, C.L.5
-
70
-
-
0347504850
-
Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of radical SAM enzymes
-
Layer G, Moser J, Heinz DW, Jahn D, Schubert WD. Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of radical SAM enzymes. EMBO J 2003;22(6214-6224).
-
(2003)
EMBO J
, vol.22
, pp. 6214-6224
-
-
Layer, G.1
Moser, J.2
Heinz, D.W.3
Jahn, D.4
Schubert, W.D.5
-
71
-
-
0042121237
-
Multiple sequence alignment with the clustal series of programs
-
Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. Multiple Sequence Alignment with the Clustal Series of Programs. Nucleic Acids Res 2003;31(13):3497-3500.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3497-3500
-
-
Chenna, R.1
Sugawara, H.2
Koike, T.3
Lopez, R.4
Gibson, T.J.5
Higgins, D.G.6
Thompson, J.D.7
-
72
-
-
0024529940
-
Structural principles of α/β barrel proteins: The packing of the interior of the sheet
-
Lesk AM, Branden C-I, Chothia C. Structural principles of α/β barrel proteins: The packing of the interior of the sheet. Proteins 1989;5:139-148.
-
(1989)
Proteins
, vol.5
, pp. 139-148
-
-
Lesk, A.M.1
Branden, C.-I.2
Chothia, C.3
-
73
-
-
1842532028
-
Locating stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation
-
Gromiha MM, Pujadas G, Magyar C, Selvaraj S, Simon I. Locating stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation. Proteins 2004;55(2):316-329.
-
(2004)
Proteins
, vol.55
, Issue.2
, pp. 316-329
-
-
Gromiha, M.M.1
Pujadas, G.2
Magyar, C.3
Selvaraj, S.4
Simon, I.5
-
74
-
-
0016244339
-
The mechanism of action of ethanolamine ammonia lyase, a B12-dependent enzyme: The participation of paramagnetic species in the catalytic deamination of 2-aminopropanol
-
Babior BM, Moss TH, Orme-Johnson WH, Beinert H. The mechanism of action of ethanolamine ammonia lyase, a B12-dependent enzyme: The participation of paramagnetic species in the catalytic deamination of 2-aminopropanol. J Biol Chem 1974;249:4537-4544.
-
(1974)
J Biol Chem
, vol.249
, pp. 4537-4544
-
-
Babior, B.M.1
Moss, T.H.2
Orme-Johnson, W.H.3
Beinert, H.4
-
75
-
-
0033597609
-
Towards a consistent mechanism for diol dehydratase catalyzed reactions: An application of the partial-proton-transfer concept
-
Smith DM, Golding BT, Radom L. Towards a consistent mechanism for diol dehydratase catalyzed reactions: An application of the partial-proton-transfer concept. J Am Chem Soc 1999;121:5700-5704.
-
(1999)
J Am Chem Soc
, vol.121
, pp. 5700-5704
-
-
Smith, D.M.1
Golding, B.T.2
Radom, L.3
-
76
-
-
0037205888
-
Computational exploration of rearrangements related to the vitamin B12-dependent ethanolamine ammonia lyase catalyzed transformation
-
Semialjac M, Schwartz H. Computational exploration of rearrangements related to the vitamin B12-dependent ethanolamine ammonia lyase catalyzed transformation. J Am Chem Soc 2002;124:8974-8983.
-
(2002)
J Am Chem Soc
, vol.124
, pp. 8974-8983
-
-
Semialjac, M.1
Schwartz, H.2
-
77
-
-
0042338528
-
Computational study on mechanistic details of the aminoethanol rearrangement catalyzed by the vitamin B12-dependent ethanolamine ammonia lyase: His and Asp/Glu acting simultaneously as catalytic auxiliaries
-
Semialjac M, Schwartz H. Computational study on mechanistic details of the aminoethanol rearrangement catalyzed by the vitamin B12-dependent ethanolamine ammonia lyase: His and Asp/Glu acting simultaneously as catalytic auxiliaries. J Org Chem 2003;68:6967-6983.
-
(2003)
J Org Chem
, vol.68
, pp. 6967-6983
-
-
Semialjac, M.1
Schwartz, H.2
-
78
-
-
1542743741
-
Role of Arg100 in the active site of adenosylcobalamin-dependent glutamate mutase
-
Xia L, Ballou DP, Marsh ENG. Role of Arg100 in the Active Site of Adenosylcobalamin-Dependent Glutamate Mutase. Biochemistry 2004;43:3238-3245.
-
(2004)
Biochemistry
, vol.43
, pp. 3238-3245
-
-
Xia, L.1
Ballou, D.P.2
Marsh, E.N.G.3
|