-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new-generation of protein database search programs
-
Altschul, S. F., T. L. Madden, A. A. Schaffer, J. H. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new-generation of protein database search programs. Nucleic Acids Res. 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.H.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
0037447834
-
Microbial communities in acid mine drainage
-
Baker, B. J., and J. F. Banfield. 2003. Microbial communities in acid mine drainage. FEMS Microbiol. Ecol. 44:139-152.
-
(2003)
FEMS Microbiol. Ecol
, vol.44
, pp. 139-152
-
-
Baker, B.J.1
Banfield, J.F.2
-
3
-
-
0023653927
-
Simultaneous determination of hemes-a, b and c from pyridine hemochrome spectra
-
Berry, E. A., and B. L. Trumpower. 1987. Simultaneous determination of hemes-a, b and c from pyridine hemochrome spectra. Anal. Biochem. 161: 1-15.
-
(1987)
Anal. Biochem
, vol.161
, pp. 1-15
-
-
Berry, E.A.1
Trumpower, B.L.2
-
4
-
-
0033831747
-
Phytogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site
-
Bond, P. L., S. P. Smriga, and J. F. Banfield. 2000. Phytogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site. Appl. Environ Microbiol. 66:3842-3849.
-
(2000)
Appl. Environ Microbiol
, vol.66
, pp. 3842-3849
-
-
Bond, P.L.1
Smriga, S.P.2
Banfield, J.F.3
-
5
-
-
0031576989
-
Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool
-
Bower, M. J., F. E. Cohen, and R. L. Dunbrack. 1997. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J. Mol. Biol. 267:1268-1282.
-
(1997)
J. Mol. Biol
, vol.267
, pp. 1268-1282
-
-
Bower, M.J.1
Cohen, F.E.2
Dunbrack, R.L.3
-
6
-
-
0017184389
-
Rapid and sensitive method for the quantitation of microgram quantities of protein utilizing principle of protein-dye binding
-
Bradford, M. M. 1976. Rapid and sensitive method for the quantitation of microgram quantities of protein utilizing principle of protein-dye binding. Anal. Biochem. 72:248-254.
-
(1976)
Anal. Biochem
, vol.72
, pp. 248-254
-
-
Bradford, M.M.1
-
7
-
-
33748312319
-
Characterization of pII family (GlnK1, GlnK2, and GlnB) protein uridylylation in response to nitrogen availability for Rhodopseudomonas palustris
-
Connelly, H. M., D. A. Pelletier, T. Y. Lu, P. K. Lankford, and R. L. Hettich. 2006. Characterization of pII family (GlnK1, GlnK2, and GlnB) protein uridylylation in response to nitrogen availability for Rhodopseudomonas palustris. Anal. Biochem. 357:93-104.
-
(2006)
Anal. Biochem
, vol.357
, pp. 93-104
-
-
Connelly, H.M.1
Pelletier, D.A.2
Lu, T.Y.3
Lankford, P.K.4
Hettich, R.L.5
-
8
-
-
19144366548
-
Acid mine drainage biogeochemistry at Iron Mountain, California
-
Druschel, G. K., B. J. Baker, T. M. Gihring, and J. F. Banfield. 2004. Acid mine drainage biogeochemistry at Iron Mountain, California. Geochem. Trans. 5:13-32.
-
(2004)
Geochem. Trans
, vol.5
, pp. 13-32
-
-
Druschel, G.K.1
Baker, B.J.2
Gihring, T.M.3
Banfield, J.F.4
-
9
-
-
17144425763
-
Practical lessons from protein structure prediction
-
Ginalski, K., N. V. Grishin, A. Godzik, and L. Rychlewski. 2005. Practical lessons from protein structure prediction. Nucleic Acids Res. 33:1874-1891.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 1874-1891
-
-
Ginalski, K.1
Grishin, N.V.2
Godzik, A.3
Rychlewski, L.4
-
10
-
-
0025726425
-
An acid-stable cytochrome in iron-oxidizing Leptospirillum ferrooxidans
-
Hart, A., J. C. Murrell, R. K. Poole, and P. R. Norris. 1991. An acid-stable cytochrome in iron-oxidizing Leptospirillum ferrooxidans. FEMS Microbiol. Lett. 81:89-94.
-
(1991)
FEMS Microbiol. Lett
, vol.81
, pp. 89-94
-
-
Hart, A.1
Murrell, J.C.2
Poole, R.K.3
Norris, P.R.4
-
11
-
-
43449096010
-
-
Jeans, C., S. W. Singer, C. S. Chan, N. C. VerBerkmoes, M. Shah, R. L. Hettich, J. F. Banfield, and M. P. Thelen. 2008. Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community. ISME J. 2:542-550.
-
Jeans, C., S. W. Singer, C. S. Chan, N. C. VerBerkmoes, M. Shah, R. L. Hettich, J. F. Banfield, and M. P. Thelen. 2008. Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community. ISME J. 2:542-550.
-
-
-
-
12
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones, D. T. 1999. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292:195-202.
-
(1999)
J. Mol. Biol
, vol.292
, pp. 195-202
-
-
Jones, D.T.1
-
13
-
-
0029154240
-
The structure of chloroplast cytochrome-c6 at 1.9 angstrom resolution: Evidence for functional oligomerization
-
Kerfeld, C. A., H. P. Anwar, R. Interrante, S. Merchant, and T. O. Yeates. 1995. The structure of chloroplast cytochrome-c6 at 1.9 angstrom resolution: evidence for functional oligomerization. J. Mol. Biol. 250:627-647.
-
(1995)
J. Mol. Biol
, vol.250
, pp. 627-647
-
-
Kerfeld, C.A.1
Anwar, H.P.2
Interrante, R.3
Merchant, S.4
Yeates, T.O.5
-
14
-
-
0014949207
-
Cleavage of structural proteins during the assembly of the head of bacteriophage T4
-
Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685.
-
(1970)
Nature
, vol.227
, pp. 680-685
-
-
Laemmli, U.K.1
-
15
-
-
34047169728
-
Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria
-
Lo, I., V. J. Denef, N. C. VerBerkmoes, M. B. Shah, D. Goltsman, G. DiBartolo, G. W. Tyson, E. E. Allen, R. J. Ram, J. C. Detter, P. Richardson, M. P. Thelen, R. L. Hettich, and J. F. Banfield. 2007. Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446:537-541.
-
(2007)
Nature
, vol.446
, pp. 537-541
-
-
Lo, I.1
Denef, V.J.2
VerBerkmoes, N.C.3
Shah, M.B.4
Goltsman, D.5
DiBartolo, G.6
Tyson, G.W.7
Allen, E.E.8
Ram, R.J.9
Detter, J.C.10
Richardson, P.11
Thelen, M.P.12
Hettich, R.L.13
Banfield, J.F.14
-
16
-
-
0025950944
-
Searching protein-sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms
-
Pearson, W. R. 1991. Searching protein-sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11:635-650.
-
(1991)
Genomics
, vol.11
, pp. 635-650
-
-
Pearson, W.R.1
-
17
-
-
21344465408
-
Community proteomics of a natural microbial biofilm
-
Ram, R. J., N. C. VerBerkmoes, M. P. Thelen, G. W. Tyson, B. J. Baker, R. C. Blake, M. Shah, R. L. Hettich, and J. F. Banfield. 2005. Community proteomics of a natural microbial biofilm. Science 308:1915-1920.
-
(2005)
Science
, vol.308
, pp. 1915-1920
-
-
Ram, R.J.1
VerBerkmoes, N.C.2
Thelen, M.P.3
Tyson, G.W.4
Baker, B.J.5
Blake, R.C.6
Shah, M.7
Hettich, R.L.8
Banfield, J.F.9
-
18
-
-
0027291015
-
Prediction of protein secondary structure at better than 70-percent accuracy
-
Rost, B., and C. Sander. 1993. Prediction of protein secondary structure at better than 70-percent accuracy. J. Mol. Biol. 232:584-599.
-
(1993)
J. Mol. Biol
, vol.232
, pp. 584-599
-
-
Rost, B.1
Sander, C.2
-
19
-
-
0014559281
-
Kinetic studies of iron oxidation by whole cells of Ferrobacillus ferrooxidans
-
Schnaitman, C. A., M. S. Korczynski, and D. G. Lundgren. 1969. Kinetic studies of iron oxidation by whole cells of Ferrobacillus ferrooxidans. J. Bacteriol. 99:552-557.
-
(1969)
J. Bacteriol
, vol.99
, pp. 552-557
-
-
Schnaitman, C.A.1
Korczynski, M.S.2
Lundgren, D.G.3
-
20
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith, T. F., and M. S. Waterman. 1981. Identification of common molecular subsequences. J. Mol. Biol. 147:195-197.
-
(1981)
J. Mol. Biol
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
21
-
-
0036393898
-
DTASelect and Contrast: Tools for assembling and comparing protein identifications from shotgun proteomics
-
Tabb, D. L., W. H. McDonald, and J. R. Yates. 2002. DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J. Proteome Res. 1:21-26.
-
(2002)
J. Proteome Res
, vol.1
, pp. 21-26
-
-
Tabb, D.L.1
McDonald, W.H.2
Yates, J.R.3
-
22
-
-
17644405163
-
DBDigger: Reorganized proteomic database identification that improves flexibility and speed
-
Tabb, D. L., C. Narasimhan, M. B. Strader, and R. L. Hettich. 2005. DBDigger: reorganized proteomic database identification that improves flexibility and speed. Anal. Chem. 77:2464-2474.
-
(2005)
Anal. Chem
, vol.77
, pp. 2464-2474
-
-
Tabb, D.L.1
Narasimhan, C.2
Strader, M.B.3
Hettich, R.L.4
-
23
-
-
0027968068
-
Clustal-W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. Clustal-W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
24
-
-
1542377296
-
Community structure and metabolism through reconstruction of microbial genomes from the environment
-
Tyson, G. W., J. Chapman, P. Hugenholtz, E. E. Allen, R. J. Ram, P. M. Richardson, V. V. Solovyev, E. M. Rubin, D. S. Rokhsar, and J. F. Banfield. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37-43.
-
(2004)
Nature
, vol.428
, pp. 37-43
-
-
Tyson, G.W.1
Chapman, J.2
Hugenholtz, P.3
Allen, E.E.4
Ram, R.J.5
Richardson, P.M.6
Solovyev, V.V.7
Rubin, E.M.8
Rokhsar, D.S.9
Banfield, J.F.10
-
25
-
-
4344634473
-
Regulation of the expression of the Acidithiobacillus ferrooxidans rus operon encoding two cytochromes c, a cytochrome oxidase and rusticyanin
-
Yarzabal, A., C. Appia-Ayme, J. Ratouchniak, and V. Bonnefoy. 2004. Regulation of the expression of the Acidithiobacillus ferrooxidans rus operon encoding two cytochromes c, a cytochrome oxidase and rusticyanin. Microbiology 150:2113-2123.
-
(2004)
Microbiology
, vol.150
, pp. 2113-2123
-
-
Yarzabal, A.1
Appia-Ayme, C.2
Ratouchniak, J.3
Bonnefoy, V.4
-
27
-
-
0036134778
-
The high-molecular-weight cytochrome c Cyc2 of Acidithiobacillus ferrooxidans is an outer membrane protein
-
Yarzabal, A., G. Brasseur, J. Ratouchniak, K. Lund, D. Lemesle-Meunier, J. A. DeMoss, and V. Bonnefoy. 2002. The high-molecular-weight cytochrome c Cyc2 of Acidithiobacillus ferrooxidans is an outer membrane protein. J. Bacteriol. 184:313-317.
-
(2002)
J. Bacteriol
, vol.184
, pp. 313-317
-
-
Yarzabal, A.1
Brasseur, G.2
Ratouchniak, J.3
Lund, K.4
Lemesle-Meunier, D.5
DeMoss, J.A.6
Bonnefoy, V.7
-
28
-
-
0042622381
-
LGA: A method for finding 3D similarities in protein structures
-
Zemla, A. 2003. LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res. 31:3370-3374.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3370-3374
-
-
Zemla, A.1
-
29
-
-
23144444980
-
AS2TS system for protein structure modeling and analysis
-
Zemla, A., C. E. Zhou, T. Slezak, T. Kuczmarski, D. Rama, C. Torres, D. Sawicka, and D. Barsky. 2005. AS2TS system for protein structure modeling and analysis. Nucleic Acids Res. 33:W111-W115.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Zemla, A.1
Zhou, C.E.2
Slezak, T.3
Kuczmarski, T.4
Rama, D.5
Torres, C.6
Sawicka, D.7
Barsky, D.8
|