-
1
-
-
0017341656
-
Microbial ecology of the gastrointestinal tract
-
Savage DC, (1977) Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol 31: 107-133.
-
(1977)
Annu Rev Microbiol
, vol.31
, pp. 107-133
-
-
Savage, D.C.1
-
2
-
-
0037425743
-
Gut flora in health and disease
-
Guarner F, Malagelada J-R, (2003) Gut flora in health and disease. Lancet 361: 512-519.
-
(2003)
Lancet
, vol.361
, pp. 512-519
-
-
Guarner, F.1
Malagelada, J.-R.2
-
3
-
-
23744440709
-
A dynamic partnership: Celebrating our gut flora
-
Sears CL, (2005) A dynamic partnership: celebrating our gut flora. Anaerobe 11: 247-251.
-
(2005)
Anaerobe
, vol.11
, pp. 247-251
-
-
Sears, C.L.1
-
4
-
-
0030969814
-
Role of intestinal bacteria in nutrient metabolism
-
Cummings JH, Macfarlane GT, (1997) Role of intestinal bacteria in nutrient metabolism. Clin Nutr 16: 3-11.
-
(1997)
Clin Nutr
, vol.16
, pp. 3-11
-
-
Cummings, J.H.1
MacFarlane, G.T.2
-
5
-
-
19344374335
-
Who controls the crowd? New findings and old questions about the intestinal microflora
-
Steinhoff U, (2005) Who controls the crowd? New findings and old questions about the intestinal microflora. Immunol Lett 99: 12-16.
-
(2005)
Immunol Lett
, vol.99
, pp. 12-16
-
-
Steinhoff, U.1
-
6
-
-
0034775213
-
Allergy development and the intestinal microflora during the first year of life
-
Björkstén B, Sepp E, Julge K, Voor T, Mikelsaar M, (2001) Allergy development and the intestinal microflora during the first year of life. J Allergy Clin Immunol 108: 516-520.
-
(2001)
J Allergy Clin Immunol
, vol.108
, pp. 516-520
-
-
Björkstén, B.1
Sepp, E.2
Julge, K.3
Voor, T.4
Mikelsaar, M.5
-
7
-
-
33845901507
-
Microbial ecology: Human gut microbes associated with obesity
-
Ley RE, Turnbaugh PJ, Klein S, Gordon JI, (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444: 1022-1023.
-
(2006)
Nature
, vol.444
, pp. 1022-1023
-
-
Ley, R.E.1
Turnbaugh, P.J.2
Klein, S.3
Gordon, J.I.4
-
8
-
-
33845874101
-
An obesity-associated gut microbiome with increased capacity for energy harvest
-
Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI, (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1031.
-
(2006)
Nature
, vol.444
, pp. 1027-1031
-
-
Turnbaugh, P.J.1
Ley, R.E.2
Mahowald, M.A.3
Magrini, V.4
Mardis, E.R.5
Gordon, J.I.6
-
9
-
-
84878287270
-
Consumption of fermented milk product with probiotic modulates brain activity
-
e4.
-
Tillisch K, Labus J, Kilpatrick L, Jiang Z, Stains J, Ebrat B, Guyonnet D, Legrain-Raspaud S, Trotin B, Naliboff B, et al., (2013) Consumption of fermented milk product with probiotic modulates brain activity. Gastroenterology 144: 1394-1401.e4.
-
(2013)
Gastroenterology
, vol.144
, pp. 1394-1401
-
-
Tillisch, K.1
Labus, J.2
Kilpatrick, L.3
Jiang, Z.4
Stains, J.5
Ebrat, B.6
Guyonnet, D.7
Legrain-Raspaud, S.8
Trotin, B.9
Naliboff, B.10
-
10
-
-
77949547790
-
Ethanolamine utilization in bacterial pathogens: Roles and regulation
-
Garsin DA, (2010) Ethanolamine utilization in bacterial pathogens: roles and regulation. Nat Rev Microbiol 8: 290-295.
-
(2010)
Nat Rev Microbiol
, vol.8
, pp. 290-295
-
-
Garsin, D.A.1
-
11
-
-
72249103848
-
Comparative genomics of ethanolamine utilization
-
Tsoy O, Ravcheev D, Mushegian A, (2009) Comparative genomics of ethanolamine utilization. J Bacteriol 191: 7157-7164.
-
(2009)
J Bacteriol
, vol.191
, pp. 7157-7164
-
-
Tsoy, O.1
Ravcheev, D.2
Mushegian, A.3
-
12
-
-
0028944586
-
Ethanolamine utilization in Salmonella typhimurium: Nucleotide sequence, protein expression, and mutational analysis of the cchA cchB eutE eutJ eutG eutH gene cluster
-
Stojiljkovic I, Bäumler AJ, Heffron F, (1995) Ethanolamine utilization in Salmonella typhimurium: nucleotide sequence, protein expression, and mutational analysis of the cchA cchB eutE eutJ eutG eutH gene cluster. J Bacteriol 177: 1357-1366.
-
(1995)
J Bacteriol
, vol.177
, pp. 1357-1366
-
-
Stojiljkovic, I.1
Bäumler, A.J.2
Heffron, F.3
-
13
-
-
0024075956
-
Ethanolamine utilization in Salmonella typhimurium
-
Roof DM, Roth JR, (1988) Ethanolamine utilization in Salmonella typhimurium. J Bacteriol 170: 3855-3863.
-
(1988)
J Bacteriol
, vol.170
, pp. 3855-3863
-
-
Roof, D.M.1
Roth, J.R.2
-
14
-
-
0017082007
-
Ethanolamine catabolism by bacteria, including Escherichia coli
-
Blackwell CM, Scarlett FA, Turner JM, (1976) Ethanolamine catabolism by bacteria, including Escherichia coli. Biochem Soc Trans 4: 495-497.
-
(1976)
Biochem Soc Trans
, vol.4
, pp. 495-497
-
-
Blackwell, C.M.1
Scarlett, F.A.2
Turner, J.M.3
-
15
-
-
0015392543
-
Non-dietary lipid in the intestinal lumen
-
Cotton PB, (1972) Non-dietary lipid in the intestinal lumen. Gut 13: 675-681.
-
(1972)
Gut
, vol.13
, pp. 675-681
-
-
Cotton, P.B.1
-
16
-
-
0014458062
-
The phosphoglyceride composition of Gram-negative bacteria and the changes in composition during growth
-
Randle CL, Albro PW, Dittmer JC, (1969) The phosphoglyceride composition of Gram-negative bacteria and the changes in composition during growth. Biochim Biophys Acta 187: 214-220.
-
(1969)
Biochim Biophys Acta
, vol.187
, pp. 214-220
-
-
Randle, C.L.1
Albro, P.W.2
Dittmer, J.C.3
-
17
-
-
0032851358
-
The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins
-
Kofoid E, Rappleye C, Stojiljkovic I, Roth J, (1999) The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. J Bacteriol 181: 5317-5329.
-
(1999)
J Bacteriol
, vol.181
, pp. 5317-5329
-
-
Kofoid, E.1
Rappleye, C.2
Stojiljkovic, I.3
Roth, J.4
-
18
-
-
65449187899
-
Detection of biochemical pathways by probabilistic matching of phyletic vectors
-
Li H, Kristensen DM, Coleman MK, Mushegian A, (2009) Detection of biochemical pathways by probabilistic matching of phyletic vectors. PLoS ONE 4: e5326.
-
(2009)
PLoS ONE
, vol.4
, pp. e5326
-
-
Li, H.1
Kristensen, D.M.2
Coleman, M.K.3
Mushegian, A.4
-
19
-
-
21844471754
-
Systematic association of genes to phenotypes by genome and literature mining
-
Korbel JO, Doerks T, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, Hooper SD, Andrade MA, Bork P, (2005) Systematic association of genes to phenotypes by genome and literature mining. PLoS Biol 3: e134.
-
(2005)
PLoS Biol
, vol.3
, pp. e134
-
-
Korbel, J.O.1
Doerks, T.2
Jensen, L.J.3
Perez-Iratxeta, C.4
Kaczanowski, S.5
Hooper, S.D.6
Andrade, M.A.7
Bork, P.8
-
20
-
-
0038575114
-
Global regulation by CsrA in Salmonella typhimurium
-
Lawhon SD, Frye JG, Suyemoto M, Porwollik S, McClelland M, Altier C, (2003) Global regulation by CsrA in Salmonella typhimurium. Mol Microbiol 48: 1633-1645.
-
(2003)
Mol Microbiol
, vol.48
, pp. 1633-1645
-
-
Lawhon, S.D.1
Frye, J.G.2
Suyemoto, M.3
Porwollik, S.4
McClelland, M.5
Altier, C.6
-
21
-
-
4344716137
-
A global role for Fis in the transcriptional control of metabolism and type III secretion in Salmonella enterica serovar Typhimurium
-
Kelly A, Goldberg MD, Carroll RK, Danino V, Hinton JCD, Dorman CJ, (2004) A global role for Fis in the transcriptional control of metabolism and type III secretion in Salmonella enterica serovar Typhimurium. Microbiology 150: 2037-2053.
-
(2004)
Microbiology
, vol.150
, pp. 2037-2053
-
-
Kelly, A.1
Goldberg, M.D.2
Carroll, R.K.3
Danino, V.4
Hinton, J.C.D.5
Dorman, C.J.6
-
22
-
-
33646011978
-
Comparison of OG1RF and an isogenic fsrB deletion mutant by transcriptional analysis: The Fsr System of Enterococcus faecalis is more than the activator of gelatinase and serine protease
-
Bourgogne A, Hilsenbeck SG, Dunny GM, Murray BE, (2006) Comparison of OG1RF and an isogenic fsrB deletion mutant by transcriptional analysis: the Fsr System of Enterococcus faecalis is more than the activator of gelatinase and serine protease. J Bacteriol 188: 2875-2884.
-
(2006)
J Bacteriol
, vol.188
, pp. 2875-2884
-
-
Bourgogne, A.1
Hilsenbeck, S.G.2
Dunny, G.M.3
Murray, B.E.4
-
23
-
-
77957157893
-
Gut inflammation provides a respiratory electron acceptor for Salmonella
-
Winter SE, Thiennimitr P, Winter MG, Butler BP, Huseby DL, Crawford RW, Russell JM, Bevins CL, Adams LG, Tsolis RM, Roth JR, Bäumler AJ,. (2010) Gut inflammation provides a respiratory electron acceptor for Salmonella. Nature 467: 426-429.
-
(2010)
Nature
, vol.467
, pp. 426-429
-
-
Winter, S.E.1
Thiennimitr, P.2
Winter, M.G.3
Butler, B.P.4
Huseby, D.L.5
Crawford, R.W.6
Russell, J.M.7
Bevins, C.L.8
Adams, L.G.9
Tsolis, R.M.10
Roth, J.R.11
Aj, B.12
-
24
-
-
80054806900
-
Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota
-
Thiennimitr P, Winter SE, Winter MG, Xavier MN, Tolstikov V, Huseby DL, Sterzenbach T, Tsolis RM, Roth JR, Bäumler AJ, (2011) Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota. Proc Natl Acad Sci U S A 108: 17480-17485.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 17480-17485
-
-
Thiennimitr, P.1
Winter, S.E.2
Winter, M.G.3
Xavier, M.N.4
Tolstikov, V.5
Huseby, D.L.6
Sterzenbach, T.7
Tsolis, R.M.8
Roth, J.R.9
Bäumler, A.J.10
-
25
-
-
79956261475
-
A breathtaking feat: To compete with the gut microbiota, Salmonella drives its host to provide a respiratory electron acceptor
-
Winter SE, Bäumler AJ, (2011) A breathtaking feat: to compete with the gut microbiota, Salmonella drives its host to provide a respiratory electron acceptor. Gut Microbes 2: 58-60.
-
(2011)
Gut Microbes
, vol.2
, pp. 58-60
-
-
Winter, S.E.1
Bäumler, A.J.2
-
26
-
-
0028808541
-
DNA polymerase I function is required for the utilization of ethanolamine, 1,2-propanediol, and propionate by Salmonella typhimurium LT2
-
Rondon MR, Horswill AR, Escalante-Semerena JC, (1995) DNA polymerase I function is required for the utilization of ethanolamine, 1,2-propanediol, and propionate by Salmonella typhimurium LT2. J Bacteriol 177: 7119-7124.
-
(1995)
J Bacteriol
, vol.177
, pp. 7119-7124
-
-
Rondon, M.R.1
Horswill, A.R.2
Escalante-Semerena, J.C.3
-
27
-
-
33645964606
-
Conserving a volatile metabolite: A role for carboxysome-like organelles in Salmonella enterica
-
Penrod JT, Roth JR, (2006) Conserving a volatile metabolite: a role for carboxysome-like organelles in Salmonella enterica. J Bacteriol 188: 2865-2874.
-
(2006)
J Bacteriol
, vol.188
, pp. 2865-2874
-
-
Penrod, J.T.1
Roth, J.R.2
-
28
-
-
84880017088
-
Evidence that a metabolic microcompartment contains and recycles private cofactor pools
-
Huseby DL, Roth JR, (2013) Evidence that a metabolic microcompartment contains and recycles private cofactor pools. J Bacteriol 195: 2864-2879.
-
(2013)
J Bacteriol
, vol.195
, pp. 2864-2879
-
-
Huseby, D.L.1
Roth, J.R.2
-
29
-
-
84867515386
-
The PduQ enzyme Is an alcohol dehydrogenase used to recycle NAD+ internally within the Pdu microcompartment of Salmonella enterica
-
Cheng S, Fan C, Sinha S, Bobik TA, (2012) The PduQ enzyme Is an alcohol dehydrogenase used to recycle NAD+ internally within the Pdu microcompartment of Salmonella enterica. PLoS ONE 7: e47144.
-
(2012)
PLoS ONE
, vol.7
, pp. e47144
-
-
Cheng, S.1
Fan, C.2
Sinha, S.3
Bobik, T.A.4
-
30
-
-
0014429342
-
Ethanolamine Deaminase, a Cobamide Coenzyme-dependent Enzyme II. Physical and chemical properties and interaction with cobamides and ethanolamine
-
Kaplan BH, Stadtman ER, (1968) Ethanolamine Deaminase, a Cobamide Coenzyme-dependent Enzyme II. Physical and chemical properties and interaction with cobamides and ethanolamine. J Biol Chem 243: 1794-1803.
-
(1968)
J Biol Chem
, vol.243
, pp. 1794-1803
-
-
Kaplan, B.H.1
Stadtman, E.R.2
-
31
-
-
4944253783
-
Identification of a reactivating factor for adenosylcobalamin-dependent ethanolamine ammonia lyase
-
Mori K, Bando R, Hieda N, Toraya T, (2004) Identification of a reactivating factor for adenosylcobalamin-dependent ethanolamine ammonia lyase. J Bacteriol 186: 6845-6854.
-
(2004)
J Bacteriol
, vol.186
, pp. 6845-6854
-
-
Mori, K.1
Bando, R.2
Hieda, N.3
Toraya, T.4
-
32
-
-
4344682568
-
The eutT gene of Salmonella enterica encodes an oxygen-labile, metal-containing ATP:corrinoid adenosyltransferase enzyme
-
Buan NR, Suh S-J, Escalante-Semerena JC, (2004) The eutT gene of Salmonella enterica encodes an oxygen-labile, metal-containing ATP:corrinoid adenosyltransferase enzyme. J Bacteriol 186: 5708-5714.
-
(2004)
J Bacteriol
, vol.186
, pp. 5708-5714
-
-
Buan, N.R.1
Suh, S.-J.2
Escalante-Semerena, J.C.3
-
33
-
-
67049117718
-
Crystal structure of the EutL shell protein of the ethanolamine ammonia lyase microcompartment
-
Sagermann M, Ohtaki A, Nikolakakis K, (2009) Crystal structure of the EutL shell protein of the ethanolamine ammonia lyase microcompartment. Proc Natl Acad Sci U S A 106: 8883-8887.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 8883-8887
-
-
Sagermann, M.1
Ohtaki, A.2
Nikolakakis, K.3
-
34
-
-
78049415865
-
Crystallographic insights into the pore structures and mechanisms of the EutL and EutM shell proteins of the ethanolamine-utilizing microcompartment of Escherichia coli
-
Takenoya M, Nikolakakis K, Sagermann M, (2010) Crystallographic insights into the pore structures and mechanisms of the EutL and EutM shell proteins of the ethanolamine-utilizing microcompartment of Escherichia coli. J Bacteriol 192: 6056-6063.
-
(2010)
J Bacteriol
, vol.192
, pp. 6056-6063
-
-
Takenoya, M.1
Nikolakakis, K.2
Sagermann, M.3
-
35
-
-
74849140487
-
Structure and mechanisms of a protein-based organelle in Escherichia coli
-
Tanaka S, Sawaya MR, Yeates TO, (2010) Structure and mechanisms of a protein-based organelle in Escherichia coli. Science 327: 81-84.
-
(2010)
Science
, vol.327
, pp. 81-84
-
-
Tanaka, S.1
Sawaya, M.R.2
Yeates, T.O.3
-
36
-
-
70350096554
-
Structure of a trimeric bacterial microcompartment shell protein, EtuB, associated with ethanol utilization in Clostridium kluyveri
-
Heldt D, Frank S, Seyedarabi A, Ladikis D, Parsons JB, Warren MJ, Pickersgill RW, (2009) Structure of a trimeric bacterial microcompartment shell protein, EtuB, associated with ethanol utilization in Clostridium kluyveri. Biochem J 423: 199-207.
-
(2009)
Biochem J
, vol.423
, pp. 199-207
-
-
Heldt, D.1
Frank, S.2
Seyedarabi, A.3
Ladikis, D.4
Parsons, J.B.5
Warren, M.J.6
Pickersgill, R.W.7
-
37
-
-
79952178155
-
Structure of PduT, a trimeric bacterial microcompartment protein with a 4Fe-4S cluster-binding site
-
Pang A, Warren MJ, Pickersgill RW, (2011) Structure of PduT, a trimeric bacterial microcompartment protein with a 4Fe-4S cluster-binding site. Acta Crystallogr D Biol Crystallogr 67: 91-96.
-
(2011)
Acta Crystallogr D Biol Crystallogr
, vol.67
, pp. 91-96
-
-
Pang, A.1
Warren, M.J.2
Pickersgill, R.W.3
-
38
-
-
78549246253
-
Structural insight into the mechanisms of transport across the Salmonella enterica Pdu microcompartment shell
-
Crowley CS, Cascio D, Sawaya MR, Kopstein JS, Bobik TA, Yeates TO, (2010) Structural insight into the mechanisms of transport across the Salmonella enterica Pdu microcompartment shell. J Biol Chem 285: 37838-37846.
-
(2010)
J Biol Chem
, vol.285
, pp. 37838-37846
-
-
Crowley, C.S.1
Cascio, D.2
Sawaya, M.R.3
Kopstein, J.S.4
Bobik, T.A.5
Yeates, T.O.6
-
39
-
-
68949220061
-
Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport
-
Klein MG, Zwart P, Bagby SC, Cai F, Chisholm SW, Heinhorst S, Cannon GC, Kerfeld CA, (2009) Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport. J Mol Biol 392: 319-333.
-
(2009)
J Mol Biol
, vol.392
, pp. 319-333
-
-
Klein, M.G.1
Zwart, P.2
Bagby, S.C.3
Cai, F.4
Chisholm, S.W.5
Heinhorst, S.6
Cannon, G.C.7
Kerfeld, C.A.8
-
40
-
-
84869431601
-
Substrate channels revealed in the trimeric Lactobacillus reuteri bacterial microcompartment shell protein PduB
-
Pang A, Liang M, Prentice MB, Pickersgill RW, (2012) Substrate channels revealed in the trimeric Lactobacillus reuteri bacterial microcompartment shell protein PduB. Acta Crystallogr D Biol Crystallogr 68: 1642-1652.
-
(2012)
Acta Crystallogr D Biol Crystallogr
, vol.68
, pp. 1642-1652
-
-
Pang, A.1
Liang, M.2
Prentice, M.B.3
Pickersgill, R.W.4
-
42
-
-
0034055545
-
Structural changes in a cryo-cooled protein crystal owing to radiation damage
-
Burmeister WP, (2000) Structural changes in a cryo-cooled protein crystal owing to radiation damage. Acta Crystallogr D Biol Crystallogr 56: 328-341.
-
(2000)
Acta Crystallogr D Biol Crystallogr
, vol.56
, pp. 328-341
-
-
Burmeister, W.P.1
-
43
-
-
12944269052
-
Specific chemical and structural damage to proteins produced by synchrotron radiation
-
Weik M, Ravelli RB, Kryger G, McSweeney S, Raves ML, Harel M, Gros P, Silman I, Kroon J, Sussman JL, (2000) Specific chemical and structural damage to proteins produced by synchrotron radiation. Proc Natl Acad Sci U S A 97: 623-628.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 623-628
-
-
Weik, M.1
Ravelli, R.B.2
Kryger, G.3
McSweeney, S.4
Raves, M.L.5
Harel, M.6
Gros, P.7
Silman, I.8
Kroon, J.9
Sussman, J.L.10
-
44
-
-
0036850996
-
Evidence for the formation of disulfide radicals in protein crystals upon X-ray irradiation
-
Weik M, Bergès J, Raves ML, Gros P, McSweeney S, Silman I, Sussman JL, Houée-Levin C, Ravelli RBG, (2002) Evidence for the formation of disulfide radicals in protein crystals upon X-ray irradiation. J Synchrotron Radiat 9: 342-346.
-
(2002)
J Synchrotron Radiat
, vol.9
, pp. 342-346
-
-
Weik, M.1
Bergès, J.2
Raves, M.L.3
Gros, P.4
McSweeney, S.5
Silman, I.6
Sussman, J.L.7
Houée-Levin, C.8
Ravelli, R.B.G.9
-
45
-
-
77950813607
-
Radiation damage in macromolecular crystallography: What is it and why should we care?
-
Garman EF, (2010) Radiation damage in macromolecular crystallography: what is it and why should we care? Acta Crystallogr D Biol Crystallogr 66: 339-351.
-
(2010)
Acta Crystallogr D Biol Crystallogr
, vol.66
, pp. 339-351
-
-
Garman, E.F.1
-
46
-
-
80053626537
-
Accessing protein conformational ensembles using roomerature X-ray crystallography
-
Fraser JS, van den Bedem H, Samelson AJ, Lang PT, Holton JM, Echols N, Alber T, (2011) Accessing protein conformational ensembles using roomerature X-ray crystallography. Proc Natl Acad Sci U S A 108: 16247-16252.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 16247-16252
-
-
Fraser, J.S.1
Van Den Bedem, H.2
Samelson, A.J.3
Lang, P.T.4
Holton, J.M.5
Echols, N.6
Alber, T.7
-
47
-
-
0035943379
-
Reversible lattice repacking illustrates the temperature dependence of macromolecular interactions
-
Juers DH, Matthews BW, (2001) Reversible lattice repacking illustrates the temperature dependence of macromolecular interactions. J Mol Biol 311: 851-862.
-
(2001)
J Mol Biol
, vol.311
, pp. 851-862
-
-
Juers, D.H.1
Matthews, B.W.2
-
48
-
-
84908221627
-
Modelling dynamics in protein crystal structures by ensemble refinement
-
Burnley BT, Afonine PV, Adams PD, Gros P, (2012) Modelling dynamics in protein crystal structures by ensemble refinement. eLife 1: e00311-e00311.
-
(2012)
ELife
, vol.1
, pp. e00311-e00311
-
-
Burnley, B.T.1
Afonine, P.V.2
Adams, P.D.3
Gros, P.4
-
49
-
-
0029011701
-
A Second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA, (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, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
51
-
-
0029949156
-
Symmetry, stability, and dynamics of multidomain and multicomponent protein systems
-
Blundell TL, Srinivasan N, (1996) Symmetry, stability, and dynamics of multidomain and multicomponent protein systems. Proc Natl Acad Sci 93: 14243-14248.
-
(1996)
Proc Natl Acad Sci
, vol.93
, pp. 14243-14248
-
-
Blundell, T.L.1
Srinivasan, N.2
-
52
-
-
0037560995
-
Radical catalysis in coenzyme B12-dependent isomerization (eliminating) reactions
-
Toraya T, (2003) Radical catalysis in coenzyme B12-dependent isomerization (eliminating) reactions. Chem Rev 103: 2095-2128.
-
(2003)
Chem Rev
, vol.103
, pp. 2095-2128
-
-
Toraya, T.1
-
53
-
-
84927559832
-
Structure of a bacterial microcompartment shell protein bound to a cobalamin cofactor
-
Thompson MC, Crowley CS, Kopstein J, Bobik TA, Yeates TO, (2014) Structure of a bacterial microcompartment shell protein bound to a cobalamin cofactor. Acta Crystallogr Sect F Struct Biol Cryst Commun 70: 1584-1590.
-
(2014)
Acta Crystallogr Sect F Struct Biol Cryst Commun
, vol.70
, pp. 1584-1590
-
-
Thompson, M.C.1
Crowley, C.S.2
Kopstein, J.3
Bobik, T.A.4
Yeates, T.O.5
-
54
-
-
33748282179
-
Multilate approach to modeling engineered disulfide bonds
-
Pellequer J-L, Chen SW, (2006) Multilate approach to modeling engineered disulfide bonds. Proteins 65: 192-202.
-
(2006)
Proteins
, vol.65
, pp. 192-202
-
-
Pellequer, J.-L.1
Chen, S.W.2
-
55
-
-
84856834259
-
Analysis and functional prediction of reactive cysteine residues
-
Marino SM, Gladyshev VN, (2012) Analysis and functional prediction of reactive cysteine residues. J Biol Chem 287: 4419-4425.
-
(2012)
J Biol Chem
, vol.287
, pp. 4419-4425
-
-
Marino, S.M.1
Gladyshev, V.N.2
-
56
-
-
0023258583
-
Tetrathionate reduction and production of hydrogen sulfide from thiosulfate
-
Barrett EL, Clark MA, (1987) Tetrathionate reduction and production of hydrogen sulfide from thiosulfate. Microbiol Rev 51: 192-205.
-
(1987)
Microbiol Rev
, vol.51
, pp. 192-205
-
-
Barrett, E.L.1
Clark, M.A.2
-
57
-
-
79953051017
-
Trimethylamine N-oxide as a versatile cryoprotective agent in macromolecular crystallography
-
Mueller-Dieckmann C, Kauffmann B, Weiss MS, (2011) Trimethylamine N-oxide as a versatile cryoprotective agent in macromolecular crystallography. J Appl Crystallogr 44: 433-436.
-
(2011)
J Appl Crystallogr
, vol.44
, pp. 433-436
-
-
Mueller-Dieckmann, C.1
Kauffmann, B.2
Weiss, M.S.3
-
58
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
Otwinowski Z, Minor W, (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276: 307-326.
-
(1997)
Methods Enzymol
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
59
-
-
79953737180
-
Overview of the CCP4 suite and current developments
-
Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AGW, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS,. (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67: 235-242.
-
(2011)
Acta Crystallogr D Biol Crystallogr
, vol.67
, pp. 235-242
-
-
Winn, M.D.1
Ballard, C.C.2
Cowtan, K.D.3
Dodson, E.J.4
Emsley, P.5
Evans, P.R.6
Keegan, R.M.7
Krissinel, E.B.8
Leslie, A.G.W.9
McCoy, A.10
McNicholas, S.J.11
Pannu, N.S.12
Potterton, E.A.13
Powell, H.R.14
Read, R.J.15
Vagin, A.16
Wilson, K.S.17
-
61
-
-
76449098262
-
PHENIX: A comprehensive Python-based system for macromolecular structure solution
-
Adams PD, Afonine PV, Bunkõczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung L-W, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH,. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66: 213-221.
-
(2010)
Acta Crystallogr D Biol Crystallogr
, vol.66
, pp. 213-221
-
-
Adams, P.D.1
Afonine, P.V.2
Bunkõczi, G.3
Chen, V.B.4
Davis, I.W.5
Echols, N.6
Headd, J.J.7
Hung, L.-W.8
Kapral, G.J.9
Grosse-Kunstleve, R.W.10
McCoy, A.J.11
Moriarty, N.W.12
Oeffner, R.13
Read, R.J.14
Richardson, D.C.15
Richardson, J.S.16
Terwilliger, T.C.17
Zwart, P.H.18
-
62
-
-
77951938696
-
Xtriage and Fest: Automatic assessment of X-ray data and substructure structure factor estimation
-
[Internet] 43. Available at.
-
Zwart PH, Grosse-Kunstleve RW, Adams PD, (2005) Xtriage and Fest: automatic assessment of X-ray data and substructure structure factor estimation. CCP4 Newsl. [Internet] 43. Available at: https://publications.lbl.gov/islandora/object/ir%3A127478/.
-
(2005)
CCP4 Newsl
-
-
Zwart, P.H.1
Grosse-Kunstleve, R.W.2
Adams, P.D.3
-
63
-
-
34447508216
-
Phaser crystallographic software
-
McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ, (2007) Phaser crystallographic software. J Appl Crystallogr 40: 658-674.
-
(2007)
J Appl Crystallogr
, vol.40
, pp. 658-674
-
-
McCoy, A.J.1
Grosse-Kunstleve, R.W.2
Adams, P.D.3
Winn, M.D.4
Storoni, L.C.5
Read, R.J.6
-
64
-
-
77949535720
-
Features and development of Coot
-
Emsley P, Lohkamp B, Scott WG, Cowtan K, (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66: 486-501.
-
(2010)
Acta Crystallogr D Biol Crystallogr
, vol.66
, pp. 486-501
-
-
Emsley, P.1
Lohkamp, B.2
Scott, W.G.3
Cowtan, K.4
-
65
-
-
84860273177
-
Towards automated crystallographic structure refinement with phenix.refine
-
Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD, (2012) Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr 68: 352-367.
-
(2012)
Acta Crystallogr D Biol Crystallogr
, vol.68
, pp. 352-367
-
-
Afonine, P.V.1
Grosse-Kunstleve, R.W.2
Echols, N.3
Headd, J.J.4
Moriarty, N.W.5
Mustyakimov, M.6
Terwilliger, T.C.7
Urzhumtsev, A.8
Zwart, P.H.9
Adams, P.D.10
-
66
-
-
70349597601
-
Electronic ligand builder and optimization workbench (eLBOW): A tool for ligand coordinate and restraint generation
-
Moriarty NW, Grosse-Kunstleve RW, Adams PD, (2009) Electronic ligand builder and optimization workbench (eLBOW): a tool for ligand coordinate and restraint generation. Acta Crystallogr D Biol Crystallogr 65: 1074-1080.
-
(2009)
Acta Crystallogr D Biol Crystallogr
, vol.65
, pp. 1074-1080
-
-
Moriarty, N.W.1
Grosse-Kunstleve, R.W.2
Adams, P.D.3
-
67
-
-
0000496875
-
Crystallographic fast Fourier transforms
-
Ten Eyck LF, (1973) Crystallographic fast Fourier transforms. Acta Crystallogr Sect A 29: 183-191.
-
(1973)
Acta Crystallogr Sect A
, vol.29
, pp. 183-191
-
-
Ten Eyck, L.F.1
-
68
-
-
2542445427
-
ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information
-
Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, Martz E, Ben-Tal N, (2003) ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19: 163-164.
-
(2003)
Bioinformatics
, vol.19
, pp. 163-164
-
-
Glaser, F.1
Pupko, T.2
Paz, I.3
Bell, R.E.4
Bechor-Shental, D.5
Martz, E.6
Ben-Tal, N.7
-
69
-
-
77954257799
-
ConSurf 2010: Calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
-
Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N, (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res. 38: W529-W533.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. W529-W533
-
-
Ashkenazy, H.1
Erez, E.2
Martz, E.3
Pupko, T.4
Ben-Tal, N.5
-
70
-
-
0035964342
-
Electrostatics of nanosystems: Application to microtubules and the ribosome
-
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA, (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci 98: 10037-10041.
-
(2001)
Proc Natl Acad Sci
, vol.98
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
72
-
-
84861425552
-
Linking crystallographic model and data quality
-
Karplus PA, Diederichs K, (2012) Linking crystallographic model and data quality. Science 336: 1030-1033.
-
(2012)
Science
, vol.336
, pp. 1030-1033
-
-
Karplus, P.A.1
Diederichs, K.2
-
73
-
-
74549178560
-
MolProbity: All-atom structure validation for macromolecular crystallography
-
Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC, (2009) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66: 12-21.
-
(2009)
Acta Crystallogr D Biol Crystallogr
, vol.66
, pp. 12-21
-
-
Chen, V.B.1
Arendall, W.B.2
Headd, J.J.3
Keedy, D.A.4
Immormino, R.M.5
Kapral, G.J.6
Murray, L.W.7
Richardson, J.S.8
Richardson, D.C.9
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