-
1
-
-
0037304408
-
Emergence of diverse biochemical activities in evolutionary conserved structural scaffolds of proteins
-
Anantharaman, V., Aravind, L., and Koonin, E. V. (2003) Emergence of diverse biochemical activities in evolutionary conserved structural scaffolds of proteins, Curr. Opin. Chem. Biol. 7, 12-20.
-
(2003)
Curr. Opin. Chem. Biol
, vol.7
, pp. 12-20
-
-
Anantharaman, V.1
Aravind, L.2
Koonin, E.V.3
-
2
-
-
24644433826
-
Fold usage on genomes and protein fold evolution
-
Abeln, S., and Deane, C. M. (2005) Fold usage on genomes and protein fold evolution, Proteins: Struct., Funct., Genet. 60, 690-700.
-
(2005)
Proteins: Struct., Funct., Genet
, vol.60
, pp. 690-700
-
-
Abeln, S.1
Deane, C.M.2
-
3
-
-
0036568328
-
Structure genomics analysis: Characteristics of atypical, common and horizontally transferred folds
-
Hegyi, H., Lin, J., Greenbaum, D., and Gerstein, M. (2002) Structure genomics analysis: Characteristics of atypical, common and horizontally transferred folds, Proteins: Struct., Funct., Genet. 47, 126-141.
-
(2002)
Proteins: Struct., Funct., Genet
, vol.47
, pp. 126-141
-
-
Hegyi, H.1
Lin, J.2
Greenbaum, D.3
Gerstein, M.4
-
4
-
-
0036384350
-
One fold with many functions: The evolutionary relationships between TIM barrel families based on their sequences, structures and functions
-
Nagano, N., Orengo, C. A., and Thornton, J. M. (2002) One fold with many functions: The evolutionary relationships between TIM barrel families based on their sequences, structures and functions, J. Mol. Biol. 321, 741-765.
-
(2002)
J. Mol. Biol
, vol.321
, pp. 741-765
-
-
Nagano, N.1
Orengo, C.A.2
Thornton, J.M.3
-
5
-
-
33746922036
-
Evoluationary genomics of the HAD superfamily: Understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes
-
Burroughs, A. M., Allen, K. N., Dunaway-Mariano, D., and Aravind, L. (2006) Evoluationary genomics of the HAD superfamily: Understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes, J. Mol. Biol. 361, 1003-1034.
-
(2006)
J. Mol. Biol
, vol.361
, pp. 1003-1034
-
-
Burroughs, A.M.1
Allen, K.N.2
Dunaway-Mariano, D.3
Aravind, L.4
-
6
-
-
0036643477
-
Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: Implications for protein evolution in the RNA world
-
Aravind, L., Anantharaman, V., and Koonin, E. V. (2002) Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: Implications for protein evolution in the RNA world, Proteins: Struct., Funct., Genet. 48, 1-14.
-
(2002)
Proteins: Struct., Funct., Genet
, vol.48
, pp. 1-14
-
-
Aravind, L.1
Anantharaman, V.2
Koonin, E.V.3
-
8
-
-
17044403057
-
Type II restriction endonucleases: Structure and mechanism
-
Pingoud, A., Fuxreiter, M., Pingoud, V., and Wende, W. (2005) Type II restriction endonucleases: Structure and mechanism, Cell. Mol. Life Sci. 62, 685-707.
-
(2005)
Cell. Mol. Life Sci
, vol.62
, pp. 685-707
-
-
Pingoud, A.1
Fuxreiter, M.2
Pingoud, V.3
Wende, W.4
-
9
-
-
25444522883
-
The PD-(D/E)XK superfamily revisited: Identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function
-
Kosinski, J., Feder, M., and Bujnicki, J. M. (2005) The PD-(D/E)XK superfamily revisited: Identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function, BMC Bioinf. 6, 172.
-
(2005)
BMC Bioinf
, vol.6
, pp. 172
-
-
Kosinski, J.1
Feder, M.2
Bujnicki, J.M.3
-
10
-
-
34047130851
-
I-Ssp6803I: The first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition
-
in press
-
Orlowski, J., Boniecki, M., and Bujnicki, J. M. (2007) I-Ssp6803I: The first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition, Bioinformatics (in press).
-
(2007)
Bioinformatics
-
-
Orlowski, J.1
Boniecki, M.2
Bujnicki, J.M.3
-
11
-
-
0035151431
-
Grouping together highly diverged PD-(D/E)XK nucleases and identification of novel superfamily members using structure-guided alignment of sequence profiles
-
Bujnicki, J. M., and Rychlewski, L. (2001) Grouping together highly diverged PD-(D/E)XK nucleases and identification of novel superfamily members using structure-guided alignment of sequence profiles, J. Mol. Microbiol. Biotechnol. 3, 69-72.
-
(2001)
J. Mol. Microbiol. Biotechnol
, vol.3
, pp. 69-72
-
-
Bujnicki, J.M.1
Rychlewski, L.2
-
12
-
-
33751098253
-
Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease
-
Cymerman, I. A., Obarska, A., Skowronek, K. J., Lubys, A., and Bujnicki, J. M. (2006) Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease, Proteins 65, 867-876.
-
(2006)
Proteins
, vol.65
, pp. 867-876
-
-
Cymerman, I.A.1
Obarska, A.2
Skowronek, K.J.3
Lubys, A.4
Bujnicki, J.M.5
-
13
-
-
0032708112
-
A novel endonuclease mechanism directly visualized for I-PpoI
-
Galburt, E. A., Chevalier, B., Tang, W., Jurica, M. S., Flick, K. E., Monnat, R. J., Jr., and Stoddard, B. L. (1999) A novel endonuclease mechanism directly visualized for I-PpoI, Nat. Struct. Biol. 6, 1096-1099.
-
(1999)
Nat. Struct. Biol
, vol.6
, pp. 1096-1099
-
-
Galburt, E.A.1
Chevalier, B.2
Tang, W.3
Jurica, M.S.4
Flick, K.E.5
Monnat Jr., R.J.6
Stoddard, B.L.7
-
14
-
-
0031456272
-
Crystallization and preliminary X-ray studies of I-PpoI: A nuclear, intron-encoded homing endonuclease from Physarum polycephalum
-
Flick, K. E., McHugh, D., Heath, J. D., Stephens, K. M., Monnat, R. J., Jr., and Stoddard, B. L. (1997) Crystallization and preliminary X-ray studies of I-PpoI: A nuclear, intron-encoded homing endonuclease from Physarum polycephalum, Protein Sci. 6, 2677-2680.
-
(1997)
Protein Sci
, vol.6
, pp. 2677-2680
-
-
Flick, K.E.1
McHugh, D.2
Heath, J.D.3
Stephens, K.M.4
Monnat Jr., R.J.5
Stoddard, B.L.6
-
15
-
-
0028186679
-
Improved plasmid vectors for the analysis of protein-induced DNA bending
-
Zwieb, C., and Adhya, S. (1994) Improved plasmid vectors for the analysis of protein-induced DNA bending, Methods Mol. Biol. 30, 281-294.
-
(1994)
Methods Mol. Biol
, vol.30
, pp. 281-294
-
-
Zwieb, C.1
Adhya, S.2
-
16
-
-
0033534185
-
Chemical mechanism of DNA cleavage by the homing endonuclease I-PpoI
-
Mannino, S. J., Jenkins, C. L., and Raines, R. T. (1999) Chemical mechanism of DNA cleavage by the homing endonuclease I-PpoI, Biochemistry 38, 16178-16186.
-
(1999)
Biochemistry
, vol.38
, pp. 16178-16186
-
-
Mannino, S.J.1
Jenkins, C.L.2
Raines, R.T.3
-
17
-
-
0034697977
-
Conformational changes and cleavage by the homing endonuclease I-PpoI: A critical role for a leucine residue in the active site
-
Galburt, E. A., Chadsey, M. S., Jurica, M. S., Chevalier, B. S., Erho, D., Tang, W., Monnat, R. J., Jr., and Stoddard, B. L. (2000) Conformational changes and cleavage by the homing endonuclease I-PpoI: A critical role for a leucine residue in the active site, J. Mol. Biol. 300, 877-887.
-
(2000)
J. Mol. Biol
, vol.300
, pp. 877-887
-
-
Galburt, E.A.1
Chadsey, M.S.2
Jurica, M.S.3
Chevalier, B.S.4
Erho, D.5
Tang, W.6
Monnat Jr., R.J.7
Stoddard, B.L.8
-
18
-
-
85083603544
-
-
Rasband, W. (1997-2006) U.S. National Institutes of Health, Bethesda, MD.
-
Rasband, W. (1997-2006) U.S. National Institutes of Health, Bethesda, MD.
-
-
-
-
19
-
-
27144505097
-
Protein Identification and Analysis Tools on the ExPASy Server
-
Walker, J. M, Ed, pp, Humana Press, Totowa, NJ
-
Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M. R., Appel, R. D., and Bairoch, A. (2005) Protein Identification and Analysis Tools on the ExPASy Server, in The Proteomics Protocols Handbook (Walker, J. M., Ed.) pp 571-607, Humana Press, Totowa, NJ.
-
(2005)
The Proteomics Protocols Handbook
, pp. 571-607
-
-
Gasteiger, E.1
Hoogland, C.2
Gattiker, A.3
Duvaud, S.4
Wilkins, M.R.5
Appel, R.D.6
Bairoch, A.7
-
20
-
-
17444453249
-
Revised UV extinction coefficients for nucleoside-5′-monophosphates and unpaired DNA and RNA
-
Cavaluzzi, M. J., and Borer, P. N. (2004) Revised UV extinction coefficients for nucleoside-5′-monophosphates and unpaired DNA and RNA, Nucleic Acids Res. 32, e13.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Cavaluzzi, M.J.1
Borer, P.N.2
-
21
-
-
0029987812
-
A comparison of measured and calculated single- and double-stranded oligodeoxynucleotide extinction coefficients
-
Kallansrud, G., and Ward, B. (1996) A comparison of measured and calculated single- and double-stranded oligodeoxynucleotide extinction coefficients, Anal. Biochem. 236, 134-138.
-
(1996)
Anal. Biochem
, vol.236
, pp. 134-138
-
-
Kallansrud, G.1
Ward, B.2
-
22
-
-
0031059866
-
Processing of X-ray Diffraction Data Collected in Oscillation Mode
-
Otwinowski, Z., and 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
-
23
-
-
0033081529
-
Rapid automated molecular replacement by evolutionary search
-
Kissinger, C. R., Gehlhaar, D. K., and Fogel, D. B. (1999) Rapid automated molecular replacement by evolutionary search, Acta Crystallogr. D55 (Part 2), 484-491.
-
(1999)
Acta Crystallogr
, vol.D55
, Issue.PART 2
, pp. 484-491
-
-
Kissinger, C.R.1
Gehlhaar, D.K.2
Fogel, D.B.3
-
24
-
-
3543012707
-
Crystallography & NMR system: A new software suite for macromolecular structure determination
-
Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination, Acta Crystallogr. D54 (Part 5), 905-921.
-
(1998)
Acta Crystallogr
, vol.D54
, Issue.PART 5
, pp. 905-921
-
-
Brunger, A.T.1
Adams, P.D.2
Clore, G.M.3
DeLano, W.L.4
Gros, P.5
Grosse-Kunstleve, R.W.6
Jiang, J.S.7
Kuszewski, J.8
Nilges, M.9
Pannu, N.S.10
Read, R.J.11
Rice, L.M.12
Simonson, T.13
Warren, G.L.14
-
25
-
-
0030586823
-
Checking your imagination: Applications of the free R value
-
Kleywegt, G. J., and Brunger, A. T. (1996) Checking your imagination: Applications of the free R value, Structure 4, 897-904.
-
(1996)
Structure
, vol.4
, pp. 897-904
-
-
Kleywegt, G.J.1
Brunger, A.T.2
-
26
-
-
0032790081
-
XtalView/Xfit: A versatile program for manipulating atomic coordinates and electron density
-
McRee, D. E. (1999) XtalView/Xfit: A versatile program for manipulating atomic coordinates and electron density, J. Struct. Biol. 125, 156-165.
-
(1999)
J. Struct. Biol
, vol.125
, pp. 156-165
-
-
McRee, D.E.1
-
27
-
-
0000243829
-
PROCHECK: A program to check the stereochemical quality of protein structures
-
Laskowski, R. J., Macarthur, M. W., Moss, D. S., and Thornton, J. M. (1993) PROCHECK: A program to check the stereochemical quality of protein structures, J. Appl. Crystallogr. 26, 283-291.
-
(1993)
J. Appl. Crystallogr
, vol.26
, pp. 283-291
-
-
Laskowski, R.J.1
Macarthur, M.W.2
Moss, D.S.3
Thornton, J.M.4
-
28
-
-
0031473847
-
SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
-
Guex, N., and Peitsch, M. C. (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling, Electrophoresis 18, 2714-2723.
-
(1997)
Electrophoresis
, vol.18
, pp. 2714-2723
-
-
Guex, N.1
Peitsch, M.C.2
-
29
-
-
0012293235
-
-
DeLano Scientific, San Carlos, CA
-
DeLano, W. L. (2002) PyMOL, DeLano Scientific, San Carlos, CA.
-
(2002)
PyMOL
-
-
DeLano, W.L.1
-
30
-
-
0002107784
-
Properties of I-PpoI: A rare-cutting intron-encoded endonuclease
-
Lowery, R., Hung, L., Knoche, K., and Bandziulis, R. (1992) Properties of I-PpoI: A rare-cutting intron-encoded endonuclease, Promega Notes 38, 8-12.
-
(1992)
Promega Notes
, vol.38
, pp. 8-12
-
-
Lowery, R.1
Hung, L.2
Knoche, K.3
Bandziulis, R.4
-
31
-
-
0027424120
-
Interaction of the intron-encoded mobility endonuclease I-PpoI with its target site
-
Ellison, E. L., and Vogt, V. M. (1993) Interaction of the intron-encoded mobility endonuclease I-PpoI with its target site, Mol. Cell. Biol. 13, 7531-7539.
-
(1993)
Mol. Cell. Biol
, vol.13
, pp. 7531-7539
-
-
Ellison, E.L.1
Vogt, V.M.2
-
32
-
-
0030041471
-
Substrate binding and turnover by the highly specific I-PpoI endonuclease
-
Wittmayer, P. K., and Raines, R. T. (1996) Substrate binding and turnover by the highly specific I-PpoI endonuclease, Biochemistry 35, 1076-1083.
-
(1996)
Biochemistry
, vol.35
, pp. 1076-1083
-
-
Wittmayer, P.K.1
Raines, R.T.2
|