-
1
-
-
33645514601
-
A previously undescribed pathway for pyrimidine catabolism
-
Loh KD, Gyaneshwar P, Markenscoff Papadimitriou E, Fong R, Kim KS, Parales R, Zhou Z, Inwood W, Kustu S.A previously undescribed pathway for pyrimidine catabolism.Proc Natl Acad Sci USA 2006;103:5114-5119.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 5114-5119
-
-
Loh, K.D.1
Gyaneshwar, P.2
Markenscoff Papadimitriou, E.3
Fong, R.4
Kim, K.S.5
Parales, R.6
Zhou, Z.7
Inwood, W.8
Kustu, S.9
-
2
-
-
35448941579
-
RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines
-
Shimada T, Hirao K, Kori A, Yamamoto K, Ishihama A.RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines.Mol Microbiol 2007;66:744-757.
-
(2007)
Mol Microbiol
, vol.66
, pp. 744-757
-
-
Shimada, T.1
Hirao, K.2
Kori, A.3
Yamamoto, K.4
Ishihama, A.5
-
3
-
-
77955961477
-
The surprising Rut pathway: an unexpected way to derive nitrogen from pyrimidines
-
Parales RE, Ingraham JL.The surprising Rut pathway: an unexpected way to derive nitrogen from pyrimidines.J Bacteriol 2010;192:4086-4088.
-
(2010)
J Bacteriol
, vol.192
, pp. 4086-4088
-
-
Parales, R.E.1
Ingraham, J.L.2
-
4
-
-
77952563607
-
Catalysis of a flavoenzyme-mediated amide hydrolysis
-
Mukherjee T, Zhang Y, Abdelwahed S, Ealick SE, Begley TP.Catalysis of a flavoenzyme-mediated amide hydrolysis.J Am Chem Soc 2010;132:5550-5551.
-
(2010)
J Am Chem Soc
, vol.132
, pp. 5550-5551
-
-
Mukherjee, T.1
Zhang, Y.2
Abdelwahed, S.3
Ealick, S.E.4
Begley, T.P.5
-
5
-
-
77955969370
-
The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems
-
Kim KS, Pelton JG, Inwood WB, Andersen U, Kustu S, Wemmer DE.The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems.J Bacteriol 2010;192:4089-4102.
-
(2010)
J Bacteriol
, vol.192
, pp. 4089-4102
-
-
Kim, K.S.1
Pelton, J.G.2
Inwood, W.B.3
Andersen, U.4
Kustu, S.5
Wemmer, D.E.6
-
6
-
-
0026540411
-
The alpha/beta hydrolase fold
-
Ollis DL, Cheah E, Cygler M, Dijkstra B, Frolow F, Franken SM, Harel M, Remington SJ, Silman I, Schrag J.The alpha/beta hydrolase fold.Protein Eng 1992;5:197-211.
-
(1992)
Protein Eng
, vol.5
, pp. 197-211
-
-
Ollis, D.L.1
Cheah, E.2
Cygler, M.3
Dijkstra, B.4
Frolow, F.5
Franken, S.M.6
Harel, M.7
Remington, S.J.8
Silman, I.9
Schrag, J.10
-
7
-
-
0032784276
-
Alpha/beta hydrolase fold enzymes: the family keeps growing
-
Nardini M, Dijkstra BW.Alpha/beta hydrolase fold enzymes: the family keeps growing.Curr Opin Struct Biol 1999;9:732-737.
-
(1999)
Curr Opin Struct Biol
, vol.9
, pp. 732-737
-
-
Nardini, M.1
Dijkstra, B.W.2
-
8
-
-
0034285515
-
Alpha/beta-hydrolase fold enzymes: structures, functions and mechanisms
-
Holmquist M.Alpha/beta-hydrolase fold enzymes: structures, functions and mechanisms.Curr Protein Pept Sci 2000;1:209-235.
-
(2000)
Curr Protein Pept Sci
, vol.1
, pp. 209-235
-
-
Holmquist, M.1
-
9
-
-
0004270170
-
-
Brooklyn, N.Y. Media, Pa.: Greene Pub. Associates; J. Wiley, order fulfillment;.
-
Frederick MA. Current protocols in molecular biology.Brooklyn, N.Y. Media, Pa.: Greene Pub. Associates; J. Wiley, order fulfillment;1987.
-
(1987)
Current protocols in molecular biology
-
-
Frederick, M.A.1
-
10
-
-
0035190121
-
Structure of Thermotoga maritima stationary phase survival protein SurE: a novel acid phosphatase
-
Zhang RG, Skarina T, Katz JE, Beasley S, Khachatryan A, Vyas S, Arrowsmith CH, Clarke S, Edwards A, Joachimiak A, Savchenko A.Structure of Thermotoga maritima stationary phase survival protein SurE: a novel acid phosphatase.Structure 2001;9:1095-1106.
-
(2001)
Structure
, vol.9
, pp. 1095-1106
-
-
Zhang, R.G.1
Skarina, T.2
Katz, J.E.3
Beasley, S.4
Khachatryan, A.5
Vyas, S.6
Arrowsmith, C.H.7
Clarke, S.8
Edwards, A.9
Joachimiak, A.10
Savchenko, A.11
-
11
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
Otwinowski Z, Minor W.Processing of X-ray diffraction data collected in oscillation mode.Method Enzymol 1997;276:307-326.
-
(1997)
Method Enzymol
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
12
-
-
33745933955
-
HKL-3000: the integration of data reduction and structure solution-from diffraction images to an initial model in minutes
-
Minor W, Cymborowski M, Otwinowski Z, Chruszcz M.HKL-3000: the integration of data reduction and structure solution-from diffraction images to an initial model in minutes.Acta Crystallogr Sect D 2006;62:859-866.
-
(2006)
Acta Crystallogr Sect D
, vol.62
, pp. 859-866
-
-
Minor, W.1
Cymborowski, M.2
Otwinowski, Z.3
Chruszcz, M.4
-
13
-
-
37549039510
-
A short history of SHELX. Acta crystallographica section A
-
Sheldrick GM.A short history of SHELX. Acta crystallographica section A.Found Crystallogr 2008;64 (Part 1):112-122.
-
(2008)
Found Crystallogr
, vol.64
, Issue.PART 1
, pp. 112-122
-
-
Sheldrick, G.M.1
-
14
-
-
77950793231
-
Experimental phasing with SHELXC/D/E: combining chain tracing with density modification
-
Sheldrick GM.Experimental phasing with SHELXC/D/E: combining chain tracing with density modification.Acta Crystallogr Sect D 2010;66 (Part 4):479-485.
-
(2010)
Acta Crystallogr Sect D
, vol.66
, Issue.PART 4
, pp. 479-485
-
-
Sheldrick, G.M.1
-
15
-
-
0002634621
-
-
OtwinowskiZ. Wolf W,EvansPR &LeslieAGW. ed.Warrington, UK:Daresbury Laboratory;.
-
Otwinowski Z.Isomorphous Replacement and Anomalous Scattering.Wolf W, Evans PR &Leslie AGW. ed.Warrington, UK:Daresbury Laboratory;1991. pp80-86.
-
(1991)
Isomorphous Replacement and Anomalous Scattering
, pp. 80-86
-
-
-
16
-
-
0032872798
-
Density modification for macromolecular phase improvement
-
Cowtan KD, Zhang KY.Density modification for macromolecular phase improvement.Prog Biophys Mol Biol 1999;72:245-270.
-
(1999)
Prog Biophys Mol Biol
, vol.72
, pp. 245-270
-
-
Cowtan, K.D.1
Zhang, K.Y.2
-
17
-
-
0032964481
-
Automated protein model building combined with iterative structure refinement
-
Perrakis A, Morris R, Lamzin VS.Automated protein model building combined with iterative structure refinement.Nat Struct Biol 1999;6:458-463.
-
(1999)
Nat Struct Biol
, vol.6
, pp. 458-463
-
-
Perrakis, A.1
Morris, R.2
Lamzin, V.S.3
-
18
-
-
0028103275
-
The CCP4 suite: programs for protein crystallography
-
The CCP4 suite: programs for protein crystallography.Acta Crystallogr Sect D 1994;50 (Part 5):760-763.
-
(1994)
Acta Crystallogr Sect D
, vol.50
, Issue.PART 5
, pp. 760-763
-
-
-
19
-
-
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 AG, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS.Overview of the CCP4 suite and current developments.Acta Crystallogr Sect D 2011;67 (Part 4):235-242.
-
(2011)
Acta Crystallogr Sect D
, vol.67
, Issue.PART 4
, 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.9
McCoy, A.10
McNicholas, S.J.11
Murshudov, G.N.12
Pannu, N.S.13
Potterton, E.A.14
Powell, H.R.15
Read, R.J.16
Vagin, A.17
Wilson, K.S.18
-
21
-
-
0036848846
-
Automated structure solution, density modification and model building
-
Terwilliger TC.Automated structure solution, density modification and model building.Acta Crystallogr Sect D 2002;58:1937-1940.
-
(2002)
Acta Crystallogr Sect D
, vol.58
, pp. 1937-1940
-
-
Terwilliger, T.C.1
-
22
-
-
13244281317
-
Coot: model-building tools for molecular graphics
-
Emsley P, Cowtan K.Coot: model-building tools for molecular graphics.Acta Crystallogr Sect D 2004;60:2126-2132.
-
(2004)
Acta Crystallogr Sect D
, vol.60
, pp. 2126-2132
-
-
Emsley, P.1
Cowtan, K.2
-
23
-
-
0030924992
-
Refinement of macromolecular structures by the maximum-likelihood method
-
Murshudov GN, Vagin AA, Dodson EJ.Refinement of macromolecular structures by the maximum-likelihood method.Acta Crystallogr Sect D 1997;53:240-255.
-
(1997)
Acta Crystallogr Sect D
, vol.53
, pp. 240-255
-
-
Murshudov, G.N.1
Vagin, A.A.2
Dodson, E.J.3
-
24
-
-
79953763877
-
REFMAC 5 for the refinement of macromolecular crystal structures
-
Garib NM, Pavol S, Andrey AL, Navraj SP, Roberto AS, Robert AN, Martyn DW, Fei L, Alexei AV.REFMAC 5 for the refinement of macromolecular crystal structures.Acta Crystallogr Sect D 2011;67:355-367.
-
(2011)
Acta Crystallogr Sect D
, vol.67
, pp. 355-367
-
-
Garib, N.M.1
Pavol, S.2
Andrey, A.L.3
Navraj, S.P.4
Roberto, A.S.5
Robert, A.N.6
Martyn, D.W.7
Fei, L.8
Alexei, A.V.9
-
25
-
-
0037441653
-
Structure validation by C alpha geometry: phi, psi and C beta deviation
-
Richardson DC, Lovell SC, Davis IW, Adrendall WB, de Bakker PIW, Word JM, Prisant MG, Richardson JS.Structure validation by C alpha geometry: phi, psi and C beta deviation.Proteins: Struct Funct Genet 2003;50:437-450.
-
(2003)
Proteins: Struct Funct Genet
, vol.50
, pp. 437-450
-
-
Richardson, D.C.1
Lovell, S.C.2
Davis, I.W.3
Adrendall, W.B.4
de Bakker, P.I.W.5
Word, J.M.6
Prisant, M.G.7
Richardson, J.S.8
-
26
-
-
16644393507
-
Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank
-
Yang H, Guranovic V, Dutta S, Feng Z, Berman HM, Westbrook JD.Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank.Acta Crystallogr Sect D 2004;60 (Part 10):1833-1839.
-
(2004)
Acta Crystallogr Sect D
, vol.60
, Issue.PART 10
, pp. 1833-1839
-
-
Yang, H.1
Guranovic, V.2
Dutta, S.3
Feng, Z.4
Berman, H.M.5
Westbrook, J.D.6
-
27
-
-
0031302358
-
Flexible protein-ligand docking by global energy optimization in internal coordinates
-
Abagyan R, Totrov M.Flexible protein-ligand docking by global energy optimization in internal coordinates.Proteins: Struct Funct Genet 1997:215-220.
-
(1997)
Proteins: Struct Funct Genet
, pp. 215-220
-
-
Abagyan, R.1
Totrov, M.2
-
28
-
-
10044222704
-
CLANS: a Java application for visualizing protein families based on pairwise similarity
-
Frickey T, Lupas A.CLANS: a Java application for visualizing protein families based on pairwise similarity.Bioinformatics 2004;20:3702-3704.
-
(2004)
Bioinformatics
, vol.20
, pp. 3702-3704
-
-
Frickey, T.1
Lupas, A.2
-
29
-
-
9144257886
-
The Pfam protein families database
-
Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR.The Pfam protein families database.Nucleic Acids Res 2004;32(Database issue):D138-D141.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.DATABASE ISSUE
-
-
Bateman, A.1
Coin, L.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.10
Studholme, D.J.11
Yeats, C.12
Eddy, S.R.13
-
30
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer 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
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
31
-
-
79951768061
-
A product analog bound form of 3-oxoadipate-enol-lactonase (PcaD) reveals a multifunctional role for the divergent cap domain
-
Bains J, Kaufman L, Farnell B, Boulanger MJ.A product analog bound form of 3-oxoadipate-enol-lactonase (PcaD) reveals a multifunctional role for the divergent cap domain.J Mol Biol 2011;406:649-658.
-
(2011)
J Mol Biol
, vol.406
, pp. 649-658
-
-
Bains, J.1
Kaufman, L.2
Farnell, B.3
Boulanger, M.J.4
-
32
-
-
0025272240
-
Rapid and sensitive sequence comparison with Fastp and Fasta
-
Pearson WR.Rapid and sensitive sequence comparison with Fastp and Fasta.Methods Enzymol 1990;183:63-98.
-
(1990)
Methods Enzymol
, vol.183
, pp. 63-98
-
-
Pearson, W.R.1
-
33
-
-
0027968068
-
Clustal-W-improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson JD, Higgins DG, Gibson TJ.Clustal-W-improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.Nucleic Acids Res 1994;22:4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
34
-
-
0002051540
-
BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
-
Hall TA.BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT.Nucleic Acids Symp 1999;41.
-
(1999)
Nucleic Acids Symp
, pp. 41
-
-
Hall, T.A.1
-
35
-
-
78651285748
-
CDD: a conserved domain database for the functional annotation of proteins
-
Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH.CDD: a conserved domain database for the functional annotation of proteins.Nucleic Acids Res 2011;39(Database issue):D225-D229.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.DATABASE ISSUE
-
-
Marchler-Bauer, A.1
Lu, S.2
Anderson, J.B.3
Chitsaz, F.4
Derbyshire, M.K.5
DeWeese-Scott, C.6
Fong, J.H.7
Geer, L.Y.8
Geer, R.C.9
Gonzales, N.R.10
Gwadz, M.11
Hurwitz, D.I.12
Jackson, J.D.13
Ke, Z.14
Lanczycki, C.J.15
Lu, F.16
Marchler, G.H.17
Mullokandov, M.18
Omelchenko, M.V.19
Robertson, C.L.20
Song, J.S.21
Thanki, N.22
Yamashita, R.A.23
Zhang, D.24
Zhang, N.25
Zheng, C.26
Bryant, S.H.27
more..
-
36
-
-
77954288774
-
Dali server: conservation mapping in 3D
-
Holm L, Rosenstrom P.Dali server: conservation mapping in 3D.Nucleic Acids Res 2010;38(Web Server issue):W545-W549.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.WEB SERVER ISSUE
-
-
Holm, L.1
Rosenstrom, P.2
-
37
-
-
13444307044
-
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
-
PART 12 PT 1
-
Krissinel E, Henrick K.Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions.Acta Crystallogr D Biol Crystallogr 2004;60 (Part 12 Pt 1):2256-2268.
-
(2004)
Acta Crystallogr D Biol Crystallogr
, vol.60
, pp. 2256-2268
-
-
Krissinel, E.1
Henrick, K.2
-
38
-
-
33750066944
-
Catalytic role for arginine 188 in the C-C hydrolase catalytic mechanism for Escherichia coli MhpC and Burkholderia xenovorans LB400 BphD
-
Li C, Li JJ, Montgomery MG, Wood SP, Bugg TD.Catalytic role for arginine 188 in the C-C hydrolase catalytic mechanism for Escherichia coli MhpC and Burkholderia xenovorans LB400 BphD.Biochemistry 2006;45:12470-12479.
-
(2006)
Biochemistry
, vol.45
, pp. 12470-12479
-
-
Li, C.1
Li, J.J.2
Montgomery, M.G.3
Wood, S.P.4
Bugg, T.D.5
-
39
-
-
33644876020
-
Pfam: clans, web tools and services
-
Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer ELL, Bateman A.Pfam: clans, web tools and services.Nucleic Acids Res 2006;34:D247-D251.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Finn, R.D.1
Mistry, J.2
Schuster-Bockler, B.3
Griffiths-Jones, S.4
Hollich, V.5
Lassmann, T.6
Moxon, S.7
Marshall, M.8
Khanna, A.9
Durbin, R.10
Eddy, S.R.11
Sonnhammer, E.L.L.12
Bateman, A.13
-
40
-
-
38549153238
-
Data growth and its impact on the SCOP database: new developments
-
Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, Chothia C, Murzin AG.Data growth and its impact on the SCOP database: new developments.Nucleic Acids Res 2008;36(Database issue):D419-D425.
-
(2008)
Nucleic Acids Res
, vol.36
, Issue.DATABASE ISSUE
-
-
Andreeva, A.1
Howorth, D.2
Chandonia, J.M.3
Brenner, S.E.4
Hubbard, T.J.5
Chothia, C.6
Murzin, A.G.7
-
41
-
-
66449084442
-
Infrastructure for the life sciences: design and implementation of the UniProt website
-
Jain E, Bairoch A, Duvaud S, Phan I, Redaschi N, Suzek BE, Martin MJ, McGarvey P, Gasteiger E.Infrastructure for the life sciences: design and implementation of the UniProt website.BMC Bioinformatics 2009;10:136.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 136
-
-
Jain, E.1
Bairoch, A.2
Duvaud, S.3
Phan, I.4
Redaschi, N.5
Suzek, B.E.6
Martin, M.J.7
McGarvey, P.8
Gasteiger, E.9
-
42
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ.Basic local alignment search tool.J Mol Biol 1990;215:403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
|