-
1
-
-
24744450331
-
The two ages of the RNA world, and the transition to the DNA world: A story of viruses and cells
-
Forterre,P. (2005) The two ages of the RNA world, and the transition to the DNA world: A story of viruses and cells. Biochimie, 87, 793-803.
-
(2005)
Biochimie
, vol.87
, pp. 793-803
-
-
Forterre, P.1
-
2
-
-
0036046771
-
Evolution of gene fusions: Horizontal transfer versus independent events
-
research0024.1-research0024.13
-
Yanai,I., Wolf,Y.I. and Koonin,E.V. (2002) Evolution of gene fusions: horizontal transfer versus independent events. Genome Biol., 3 research0024.1-research0024.13.
-
(2002)
Genome Biol
, vol.3
-
-
Yanai, I.1
Wolf, Y.I.2
Koonin, E.V.3
-
3
-
-
23844497214
-
Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell
-
Makarova,K.S., Wolf,Y.I., Mekhedov,S.L., Mirkin,B.G. and Koonin,E.V. (2005) Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell. Nucleic Acids Res., 33, 4626-4638.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 4626-4638
-
-
Makarova, K.S.1
Wolf, Y.I.2
Mekhedov, S.L.3
Mirkin, B.G.4
Koonin, E.V.5
-
4
-
-
0033199713
-
Did DNA replication evolve twice independently?
-
Leipe,D.D., Aravind,L. and Koonin,E.V. (1999) Did DNA replication evolve twice independently? Nucleic Acids Res., 27, 3389-3401.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 3389-3401
-
-
Leipe, D.D.1
Aravind, L.2
Koonin, E.V.3
-
5
-
-
23644448872
-
Origins of DNA replication in the three domains of life
-
Robinson,N.P. and Bell,S.D. (2005) Origins of DNA replication in the three domains of life. FEBS J., 272, 3757-3766.
-
(2005)
FEBS J
, vol.272
, pp. 3757-3766
-
-
Robinson, N.P.1
Bell, S.D.2
-
6
-
-
0029163487
-
Structural and functional similarities of prokaryotic and eukaryotic DNA polymerase sliding clamps
-
Kelman,Z. and O'Donnell,M. (1995) Structural and functional similarities of prokaryotic and eukaryotic DNA polymerase sliding clamps. Nucleic Acids Res., 23, 3613-3620.
-
(1995)
Nucleic Acids Res
, vol.23
, pp. 3613-3620
-
-
Kelman, Z.1
O'Donnell, M.2
-
7
-
-
34248220998
-
Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases
-
Koonin,E.V. (2006) Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases. Biol. Direct., 1, 39.
-
(2006)
Biol. Direct
, vol.1
, pp. 39
-
-
Koonin, E.V.1
-
8
-
-
0027217643
-
Compilation, alignment, and phylogenetic relationships of DNA polymerases
-
Braithwaite,D.K. and Ito,J. (1993) Compilation, alignment, and phylogenetic relationships of DNA polymerases. Nucleic Acids Res., 21, 787-802.
-
(1993)
Nucleic Acids Res
, vol.21
, pp. 787-802
-
-
Braithwaite, D.K.1
Ito, J.2
-
9
-
-
0033048698
-
A novel family of DNA-polymerase-associated B subunits
-
Mäkiniemi,M., Pospiech,H., Kilpeläinen,S., Jokela,M., Vihinen,M. and Syväoja,J.E. (1999) A novel family of DNA-polymerase-associated B subunits. Trends Biochem. Sci., 24, 14-16.
-
(1999)
Trends Biochem. Sci
, vol.24
, pp. 14-16
-
-
Mäkiniemi, M.1
Pospiech, H.2
Kilpeläinen, S.3
Jokela, M.4
Vihinen, M.5
Syväoja, J.E.6
-
10
-
-
0032529457
-
Phosphoesterase domains associated with DNA polymerases of diverse origins
-
Aravind,L. and Koonin,E.V. (1998) Phosphoesterase domains associated with DNA polymerases of diverse origins. Nucleic Acids Res., 26 3746-3752.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 3746-3752
-
-
Aravind, L.1
Koonin, E.V.2
-
11
-
-
0033941641
-
Protein fold recognition using sequence profiles and its application in structural genomics
-
Koonin,E.V., Wolf,Y.I. and Aravind,L. (2000) Protein fold recognition using sequence profiles and its application in structural genomics. Adv. Protein Chem., 54, 245-275.
-
(2000)
Adv. Protein Chem
, vol.54
, pp. 245-275
-
-
Koonin, E.V.1
Wolf, Y.I.2
Aravind, L.3
-
12
-
-
2342597828
-
Characterization of the 3′ exonuclease subunit DP1 of Methanococcus jannaschii replicative DNA polymerase D
-
Jokela,M., Eskelinen,A., Pospiech,H., Rouvinen,J. and Syväoja,J.E. (2004) Characterization of the 3′ exonuclease subunit DP1 of Methanococcus jannaschii replicative DNA polymerase D. Nucleic Acids Res., 32, 2430-2440.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 2430-2440
-
-
Jokela, M.1
Eskelinen, A.2
Pospiech, H.3
Rouvinen, J.4
Syväoja, J.E.5
-
13
-
-
1542601166
-
DNA polymerase epsilon - more than a polymerase
-
Pospiech,H. and Syväoja,J.E. (2003) DNA polymerase epsilon - more than a polymerase. ScientificWorldJournal, 3, 87-104.
-
(2003)
ScientificWorldJournal
, vol.3
, pp. 87-104
-
-
Pospiech, H.1
Syväoja, J.E.2
-
14
-
-
1642351959
-
Distinct roles of DNA polymerases delta and epsilon at the replication fork in Xenopus egg extracts
-
Fukui,T., Yamauchi,K., Muroya,T., Akiyama,M., Maki,H., Sugino,A. and Waga,S. (2004) Distinct roles of DNA polymerases delta and epsilon at the replication fork in Xenopus egg extracts. Genes Cells, 9, 179-191.
-
(2004)
Genes Cells
, vol.9
, pp. 179-191
-
-
Fukui, T.1
Yamauchi, K.2
Muroya, T.3
Akiyama, M.4
Maki, H.5
Sugino, A.6
Waga, S.7
-
15
-
-
33745201206
-
Distinctive activities of DNA polymerases during human DNA replication
-
Rytkönen,A.K., Vaara,M., Nethanel,T., Kaufmann,G., Sormunen,R., Läärs̈a,E., Nasheuer,H.P., Rahmeh,A., Lee,M.Y., Syväoja,J.E. and Pospiech,H. (2006) Distinctive activities of DNA polymerases during human DNA replication. FEBS J., 273, 2984-3001.
-
(2006)
FEBS J
, vol.273
, pp. 2984-3001
-
-
Rytkönen, A.K.1
Vaara, M.2
Nethanel, T.3
Kaufmann, G.4
Sormunen, R.5
Läärs̈a, E.6
Nasheuer, H.P.7
Rahmeh, A.8
Lee, M.Y.9
Syväoja, J.E.10
Pospiech, H.11
-
16
-
-
34447336941
-
Yeast DNA polymerase epsilon participates in leading-strand DNA replication
-
Pursell,Z.F., Isoz,I., Lundström,E.B., Johansson,E. and Kunkel,T.A. (2007) Yeast DNA polymerase epsilon participates in leading-strand DNA replication. Science, 317, 127-130.
-
(2007)
Science
, vol.317
, pp. 127-130
-
-
Pursell, Z.F.1
Isoz, I.2
Lundström, E.B.3
Johansson, E.4
Kunkel, T.A.5
-
17
-
-
30044434363
-
Structure of Saccharomyces cerevisiae DNA polymerase epsilon by cryo-electron microscopy
-
Asturias,F.J., Cheung,I.K., Sabouri,N., Chilkova,O., Wepplo,D. and Johansson,E. (2006) Structure of Saccharomyces cerevisiae DNA polymerase epsilon by cryo-electron microscopy. Nat. Struct. Mol. Biol., 13, 35-43.
-
(2006)
Nat. Struct. Mol. Biol
, vol.13
, pp. 35-43
-
-
Asturias, F.J.1
Cheung, I.K.2
Sabouri, N.3
Chilkova, O.4
Wepplo, D.5
Johansson, E.6
-
18
-
-
0034672325
-
Estimation of protein secondary structure from circular dichroism spectra: Comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set
-
Sreerama,N. and Woody,R.W. (2000) Estimation of protein secondary structure from circular dichroism spectra: Comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set. Anal. Biochem., 287, 252-260.
-
(2000)
Anal. Biochem
, vol.287
, pp. 252-260
-
-
Sreerama, N.1
Woody, R.W.2
-
19
-
-
0004040543
-
-
San Francisco, University of California University of California, San Francisco
-
Goddard,T.D. and Kneller,D.G. (2004) Sparky 3., San Francisco, University of California University of California, San Francisco.
-
(2004)
Sparky 3
-
-
Goddard, T.D.1
Kneller, D.G.2
-
20
-
-
0347722841
-
Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients
-
Sattler,M., Schleucher,J. and Griesinger,C. (1999) Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Progr. NMR Spectr., 34, 93-158.
-
(1999)
Progr. NMR Spectr
, vol.34
, pp. 93-158
-
-
Sattler, M.1
Schleucher, J.2
Griesinger, C.3
-
21
-
-
0036360446
-
Intraresidual HNCA: An experiment for correlating only intraresidual backbone resonances
-
Permi,P. (2002) Intraresidual HNCA: An experiment for correlating only intraresidual backbone resonances. J. Biomol. NMR, 23, 201-209.
-
(2002)
J. Biomol. NMR
, vol.23
, pp. 201-209
-
-
Permi, P.1
-
23
-
-
0028541866
-
Backbone 1H and 15N resonance assignments of the N-terminal SH3 domain of drk in folded and unfolded states using enhancedsensitivity pulsed field gradient NMR techniques
-
Zhang,O., Kay,L.E., Olivier,J.P. and Forman-Kay,J.D. (1994) Backbone 1H and 15N resonance assignments of the N-terminal SH3 domain of drk in folded and unfolded states using enhancedsensitivity pulsed field gradient NMR techniques. J. Biomol. NMR, 4, 845-858.
-
(1994)
J. Biomol. NMR
, vol.4
, pp. 845-858
-
-
Zhang, O.1
Kay, L.E.2
Olivier, J.P.3
Forman-Kay, J.D.4
-
25
-
-
0036308102
-
Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA
-
Herrmann,T., Guntert,P. and Wuthrich,K. (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J. Mol. Biol. 319, 209-227.
-
(2002)
J. Mol. Biol
, vol.319
, pp. 209-227
-
-
Herrmann, T.1
Guntert, P.2
Wuthrich, K.3
-
26
-
-
23444454552
-
The Amber biomolecular simulation programs
-
Case,D.A., Cheatham,T.E. III, Darden,T., Gohlke,H., Luo,R., Merz,K.M. Jr, Onufriev,A., Simmerling,C., Wang,B. and Woods,R.J. (2005) The Amber biomolecular simulation programs. J. Comp. Chem., 26, 1668-1688.
-
(2005)
J. Comp. Chem
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham III, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz Jr, K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
27
-
-
0030339738
-
AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR
-
Laskowski,R.A., Rullmannn,J.A., MacArthur,M.W., Kaptein,R. and Thornton,J.M. (1996) AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR, 8 477-486.
-
(1996)
J. Biomol. NMR
, vol.8
, pp. 477-486
-
-
Laskowski, R.A.1
Rullmannn, J.A.2
MacArthur, M.W.3
Kaptein, R.4
Thornton, J.M.5
-
28
-
-
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., Higgins,D.G. and Gibson,T.J. (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
-
29
-
-
3242885293
-
The PredictProtein server
-
Rost,B., Yachdav,G. and Liu,J. (2004) The PredictProtein server. Nucleic Acids Res., 32, W321-W326.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Rost, B.1
Yachdav, G.2
Liu, J.3
-
30
-
-
0002511466
-
GeneDoc: Analysis and visualization of genetic variation
-
Nicholas,K.B., Nicholas,H.B. Jr and Deerfield,D.W. II (1997) GeneDoc: Analysis and visualization of genetic variation. Embnew. News, 4, 14.
-
(1997)
Embnew. News
, vol.4
, pp. 14
-
-
Nicholas, K.B.1
Nicholas Jr, H.B.2
Deerfield II, D.W.3
-
31
-
-
0027440362
-
Protein structure comparison by alignment of distance matrices
-
Holm,L. and Sander,C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
-
(1993)
J. Mol. Biol
, vol.233
, pp. 123-138
-
-
Holm, L.1
Sander, C.2
-
32
-
-
0033824470
-
DaliLite workbench for protein structure comparison
-
Holm,L. and Park,J. (2000) DaliLite workbench for protein structure comparison. Bioinformatics, 16, 566-567.
-
(2000)
Bioinformatics
, vol.16
, pp. 566-567
-
-
Holm, L.1
Park, J.2
-
33
-
-
0037246767
-
The CATH database: An extended protein family resource for structural and functional genomics
-
Pearl,F.M., Bennett,C.F., Bray,J.E., Harrison,A.P., Martin,N., Shepherd,A., Sillitoe,I., Thornton,J. and Orengo,C.A. (2003) The CATH database: An extended protein family resource for structural and functional genomics. Nucleic Acids Res., 31, 452-455.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 452-455
-
-
Pearl, F.M.1
Bennett, C.F.2
Bray, J.E.3
Harrison, A.P.4
Martin, N.5
Shepherd, A.6
Sillitoe, I.7
Thornton, J.8
Orengo, C.A.9
-
34
-
-
0029881007
-
MOLMOL: A program for display and analysis of macromolecular structures
-
Koradi,R., Billeter,M. and Wuthrich,K. (1996) MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graph., 14, 29-32.
-
(1996)
J. Mol. Graph
, vol.14
, pp. 29-32
-
-
Koradi, R.1
Billeter, M.2
Wuthrich, K.3
-
35
-
-
0042622380
-
SWISSMODEL: An automated protein homology-modeling server
-
Schwede,T., Kopp,J., Guex,N. and Peitsch,M.C. (2003) SWISSMODEL: An automated protein homology-modeling server. Nucleic Acids Res., 31, 3381-3385.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3381-3385
-
-
Schwede, T.1
Kopp, J.2
Guex, N.3
Peitsch, M.C.4
-
36
-
-
34547575995
-
A server and database for dipole moments of proteins
-
Felder,C.E., Prilusky,J., Silman,I. and Sussman,J.L. (2007) A server and database for dipole moments of proteins. Nucleic Acids Res., 35 W512-W521.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Felder, C.E.1
Prilusky, J.2
Silman, I.3
Sussman, J.L.4
-
37
-
-
23144452044
-
The HHpred interactive server for protein homology detection and structure prediction
-
Söding,J., Biegert,A. and Lupas,A.N. (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res., 33, W244-W248.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Söding, J.1
Biegert, A.2
Lupas, A.N.3
-
38
-
-
0033027208
-
Completeness of NOEs in protein structure: A statistical analysis of NMR
-
Doreleijers,J.F., Raves,M.L., Rullmann,T. and Kaptein,R. (1999) Completeness of NOEs in protein structure: A statistical analysis of NMR. J. Biomol. NMR, 14, 123-132.
-
(1999)
J. Biomol. NMR
, vol.14
, pp. 123-132
-
-
Doreleijers, J.F.1
Raves, M.L.2
Rullmann, T.3
Kaptein, R.4
-
39
-
-
0032969563
-
AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes
-
Neuwald,A.F., Aravind,L., Spouge,J.L. and Koonin,E.V. (1999) AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res., 9, 27-43.
-
(1999)
Genome Res
, vol.9
, pp. 27-43
-
-
Neuwald, A.F.1
Aravind, L.2
Spouge, J.L.3
Koonin, E.V.4
-
40
-
-
21744446127
-
AAA+ proteins: Have engine, will work
-
Hanson,P.I. and Whiteheart,S.W. (2005) AAA+ proteins: Have engine, will work. Nat. Rev. Mol. Cell Biol., 6, 519-529.
-
(2005)
Nat. Rev. Mol. Cell Biol
, vol.6
, pp. 519-529
-
-
Hanson, P.I.1
Whiteheart, S.W.2
-
41
-
-
33745041480
-
Evolutionary relationships and structural mechanisms of AAA+ proteins
-
Erzberger,J.P. and Berger,J.M. (2006) Evolutionary relationships and structural mechanisms of AAA+ proteins. Annu. Rev. Biophys. Biomol. Struct., 35, 93-114.
-
(2006)
Annu. Rev. Biophys. Biomol. Struct
, vol.35
, pp. 93-114
-
-
Erzberger, J.P.1
Berger, J.M.2
-
42
-
-
1642325936
-
Evolutionary history and higher order classification of AAA+ ATPases
-
Iyer,L.M., Leipe,D.D., Koonin,E.V. and Aravind,L. (2004) Evolutionary history and higher order classification of AAA+ ATPases. J. Struct. Biol., 146, 11-31.
-
(2004)
J. Struct. Biol
, vol.146
, pp. 11-31
-
-
Iyer, L.M.1
Leipe, D.D.2
Koonin, E.V.3
Aravind, L.4
-
43
-
-
33749236397
-
Classification of AAA+ proteins
-
Ammelburg,M., Frickey,T. and Lupas,A.N. (2006) Classification of AAA+ proteins. J. Struct. Biol., 156, 2-11.
-
(2006)
J. Struct. Biol
, vol.156
, pp. 2-11
-
-
Ammelburg, M.1
Frickey, T.2
Lupas, A.N.3
-
44
-
-
0037271207
-
Common domains in the initiators of DNA replication in Bacteria, Archaea and Eukarya: Combined structural, functional and phylogenetic perspectives
-
Giraldo,R. (2003) Common domains in the initiators of DNA replication in Bacteria, Archaea and Eukarya: Combined structural, functional and phylogenetic perspectives. FEMS Microbiol. Rev., 26, 533-554.
-
(2003)
FEMS Microbiol. Rev
, vol.26
, pp. 533-554
-
-
Giraldo, R.1
-
45
-
-
23344439328
-
Evolutionary clues to eukaryotic DNA clamp-loading mechanisms: Analysis of the functional constraints imposed on replication factor C AAA+ ATPases
-
Neuwald,A.F. (2005) Evolutionary clues to eukaryotic DNA clamp-loading mechanisms: Analysis of the functional constraints imposed on replication factor C AAA+ ATPases. Nucleic Acids Res., 33, 3614-3628.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 3614-3628
-
-
Neuwald, A.F.1
-
46
-
-
0030666224
-
Crystal structure of the delta subunit of the clamp-loader complex of E. coli DNA polymerase III
-
Guenther,B., Onrust,R., Sali,A., O'Donnell,M. and Kuriyan,J. (1997) Crystal structure of the delta subunit of the clamp-loader complex of E. coli DNA polymerase III. Cell, 91, 335-345.
-
(1997)
Cell
, vol.91
, pp. 335-345
-
-
Guenther, B.1
Onrust, R.2
Sali, A.3
O'Donnell, M.4
Kuriyan, J.5
-
47
-
-
0031566432
-
Recognition of analogous and homologous protein folds: Analysis of sequence and structure conservation
-
Russell,R.B., Saqi,M.A., Sayle,R.A., Bates,P.A. and Sternberg,M.J. (1997) Recognition of analogous and homologous protein folds: Analysis of sequence and structure conservation. J. Mol. Biol., 269, 423-439.
-
(1997)
J. Mol. Biol
, vol.269
, pp. 423-439
-
-
Russell, R.B.1
Saqi, M.A.2
Sayle, R.A.3
Bates, P.A.4
Sternberg, M.J.5
-
48
-
-
0033120222
-
Identification of homologous core structures
-
Matsuo,Y. and Bryant,S.H. (1999) Identification of homologous core structures. Proteins, 35, 70-79.
-
(1999)
Proteins
, vol.35
, pp. 70-79
-
-
Matsuo, Y.1
Bryant, S.H.2
-
49
-
-
0034753838
-
Identification of homology in protein structure classification
-
Dietmann,S. and Holm,L. (2001) Identification of homology in protein structure classification. Nat. Struct. Biol., 8, 953-957.
-
(2001)
Nat. Struct. Biol
, vol.8
, pp. 953-957
-
-
Dietmann, S.1
Holm, L.2
-
50
-
-
0344837306
-
Conservation of electrostatic properties within enzyme families and superfamilies
-
Livesay,D.R., Jambeck,P., Rojnuckarin,A. and Subramaniam,S. (2003) Conservation of electrostatic properties within enzyme families and superfamilies. Biochemistry, 42, 3464-3473.
-
(2003)
Biochemistry
, vol.42
, pp. 3464-3473
-
-
Livesay, D.R.1
Jambeck, P.2
Rojnuckarin, A.3
Subramaniam, S.4
-
51
-
-
34047243852
-
On the origin of the histone fold
-
Alva,V., Ammelburg,M., Soding,J. and Lupas,A.N. (2007) On the origin of the histone fold. BMC Struct. Biol., 7, 17.
-
(2007)
BMC Struct. Biol
, vol.7
, pp. 17
-
-
Alva, V.1
Ammelburg, M.2
Soding, J.3
Lupas, A.N.4
|