-
1
-
-
84861130663
-
MACiE: Exploring the diversity of biochemical reactions
-
Holliday, G. L., Andreini, C., Fischer, J. D., Rahman, S. A., Almonacid, D. E., Williams, S. T. and Pearson, W. R. (2012) MACiE: exploring the diversity of biochemical reactions. Nucleic Acids Res., 40, D783-D789.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D783-D789
-
-
Holliday, G.L.1
Andreini, C.2
Fischer, J.D.3
Rahman, S.A.4
Almonacid, D.E.5
Williams, S.T.6
Pearson, W.R.7
-
2
-
-
84937603864
-
Protein function from its emergence to diversity in contemporary proteins
-
Goncearenco, A. and Berezovsky, I. N. (2015) Protein function from its emergence to diversity in contemporary proteins. Phys. Biol., 12, 045002.
-
(2015)
Phys. Biol.
, vol.12
, pp. 045002
-
-
Goncearenco, A.1
Berezovsky, I.N.2
-
3
-
-
77958511659
-
The structures and physicochemical properties of organic cofactors in biocatalysis
-
Fischer, J. D., Holliday, G. L., Rahman, S. A. and Thornton, J. M. (2010) The structures and physicochemical properties of organic cofactors in biocatalysis. J. Mol. Biol., 403, 803-824.
-
(2010)
J. Mol. Biol.
, vol.403
, pp. 803-824
-
-
Fischer, J.D.1
Holliday, G.L.2
Rahman, S.A.3
Thornton, J.M.4
-
4
-
-
77957234003
-
The CoFactor database: Organic cofactors in enzyme catalysis
-
Fischer, J. D., Holliday, G. L. and Thornton, J. M. (2010) The CoFactor database: organic cofactors in enzyme catalysis. Bioinformatics, 26, 2496-2497.
-
(2010)
Bioinformatics
, vol.26
, pp. 2496-2497
-
-
Fischer, J.D.1
Holliday, G.L.2
Thornton, J.M.3
-
5
-
-
0001607723
-
Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold
-
Walker, J. E., Saraste, M., Runswick, M. J. and Gay, N. J. (1982) Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J., 1, 945-951.
-
(1982)
EMBO J.
, vol.1
, pp. 945-951
-
-
Walker, J.E.1
Saraste, M.2
Runswick, M.J.3
Gay, N.J.4
-
6
-
-
0029914905
-
Active site comparisons highlight structural similarities between myosin and other P-loop proteins
-
Smith, C. A. and Rayment, I. (1996) Active site comparisons highlight structural similarities between myosin and other P-loop proteins. Biophys. J., 70, 1590-1602.
-
(1996)
Biophys. J.
, vol.70
, pp. 1590-1602
-
-
Smith, C.A.1
Rayment, I.2
-
7
-
-
0032972775
-
Structural motif of phosphate-binding site common to various protein superfamilies: All-against-all structural comparison of protein-mononucleotide complexes
-
Kinoshita, K., Sadanami, K., Kidera, A. and Go, N. (1999) Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of protein-mononucleotide complexes. Protein Eng., 12, 11-14.
-
(1999)
Protein Eng.
, vol.12
, pp. 11-14
-
-
Kinoshita, K.1
Sadanami, K.2
Kidera, A.3
Go, N.4
-
8
-
-
3042809615
-
Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: An automated all-against-all structural comparison using geometric matching
-
Brakoulias, A. and Jackson, R. M. (2004) Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: an automated all-against-all structural comparison using geometric matching. Proteins, 56, 250-260.
-
(2004)
Proteins
, vol.56
, pp. 250-260
-
-
Brakoulias, A.1
Jackson, R.M.2
-
9
-
-
77954364272
-
Modular architecture of nucleotide-binding pockets
-
Gherardini, P. F., Ausiello, G., Russell, R. B. and Helmer-Citterich, M. (2010) Modular architecture of nucleotide-binding pockets. Nucleic Acids Res., 38, 3809-3816.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 3809-3816
-
-
Gherardini, P.F.1
Ausiello, G.2
Russell, R.B.3
Helmer-Citterich, M.4
-
10
-
-
84855711573
-
Cofactor-binding sites in proteins of deviating sequence: Comparative analysis and clustering in torsion angle, cavity, and fold space
-
Stegemann, B. and Klebe, G. (2012) Cofactor-binding sites in proteins of deviating sequence: comparative analysis and clustering in torsion angle, cavity, and fold space. Proteins, 80, 626-648.
-
(2012)
Proteins
, vol.80
, pp. 626-648
-
-
Stegemann, B.1
Klebe, G.2
-
11
-
-
44449139387
-
Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments
-
Xie, L. and Bourne, P. E. (2008) Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc. Natl. Acad. Sci. U. S. A., 105, 5441-5446.
-
(2008)
Proc. Natl. Acad. Sci. U. S. A.
, vol.105
, pp. 5441-5446
-
-
Xie, L.1
Bourne, P.E.2
-
12
-
-
0030893657
-
NADP-dependent enzymes. I: Conserved stereochemistry of cofactor binding
-
Carugo, O. and Argos, P. (1997) NADP-dependent enzymes. I: Conserved stereochemistry of cofactor binding. Proteins, 28, 10-28.
-
(1997)
Proteins
, vol.28
, pp. 10-28
-
-
Carugo, O.1
Argos, P.2
-
13
-
-
0030972646
-
NADP-dependent enzymes. II: Evolution of the mono- and dinucleotide binding domains
-
Carugo, O. and Argos, P. (1997) NADP-dependent enzymes. II: Evolution of the mono- and dinucleotide binding domains. Proteins, 28, 29-40.
-
(1997)
Proteins
, vol.28
, pp. 29-40
-
-
Carugo, O.1
Argos, P.2
-
14
-
-
0142154391
-
'Acceptor-donor-acceptor' motifs recognize the Watson-Crick, Hoogsteen and Sugar 'donor-acceptor-donor' edges of adenine and adenosine-containing ligands
-
Denessiouk, K. A. and Johnson, M. S. (2003) 'Acceptor-donor-acceptor' motifs recognize the Watson-Crick, Hoogsteen and Sugar 'donor-acceptor-donor' edges of adenine and adenosine-containing ligands. J. Mol. Biol., 333, 1025-1043.
-
(2003)
J. Mol. Biol.
, vol.333
, pp. 1025-1043
-
-
Denessiouk, K.A.1
Johnson, M.S.2
-
15
-
-
0034854206
-
Sequence-structure analysis of FAD-containing proteins
-
Dym, O. and Eisenberg, D. (2001) Sequence-structure analysis of FAD-containing proteins. Protein Sci., 10, 1712-1728.
-
(2001)
Protein Sci.
, vol.10
, pp. 1712-1728
-
-
Dym, O.1
Eisenberg, D.2
-
16
-
-
0035882572
-
Adenine recognition: A motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins
-
Denessiouk, K. A., Rantanen, V. V. and Johnson, M. S. (2001) Adenine recognition: a motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins. Proteins, 44, 282-291.
-
(2001)
Proteins
, vol.44
, pp. 282-291
-
-
Denessiouk, K.A.1
Rantanen, V.V.2
Johnson, M.S.3
-
17
-
-
0036396532
-
GXXXG and GXXXA motifs stabilize FAD and NAD (P)-binding Rossmann folds through C (alpha)-H···O hydrogen bonds and van der waals interactions
-
Kleiger, G. and Eisenberg, D. (2002) GXXXG and GXXXA motifs stabilize FAD and NAD (P)-binding Rossmann folds through C (alpha)-H···O hydrogen bonds and van der waals interactions. J. Mol. Biol., 323, 69-76.
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 69-76
-
-
Kleiger, G.1
Eisenberg, D.2
-
18
-
-
0028279385
-
The functions and consensus motifs of nine types of peptide segments that form different types of nucleotide-binding sites
-
Traut, T. W. (1994) The functions and consensus motifs of nine types of peptide segments that form different types of nucleotide-binding sites. Euro. J. Biochem., 222, 9-19.
-
(1994)
Euro. J. Biochem.
, vol.222
, pp. 9-19
-
-
Traut, T.W.1
-
19
-
-
84879386377
-
Computational approaches for predicting the binding sites and understanding the recognition mechanism of protein-DNA complexes
-
Gromiha, M. M. and Nagarajan, R. (2013) Computational approaches for predicting the binding sites and understanding the recognition mechanism of protein-DNA complexes. Adv. Protein Chem. Struct. Biol., 91, 65-99.
-
(2013)
Adv. Protein Chem. Struct. Biol.
, vol.91
, pp. 65-99
-
-
Gromiha, M.M.1
Nagarajan, R.2
-
20
-
-
77956555559
-
Prototypes of elementary functional loops unravel evolutionary connections between protein functions
-
Goncearenco, A. and Berezovsky, I. N. (2010) Prototypes of elementary functional loops unravel evolutionary connections between protein functions. Bioinformatics, 26, i497-503.
-
(2010)
Bioinformatics
, vol.26
, pp. i497-i503
-
-
Goncearenco, A.1
Berezovsky, I.N.2
-
21
-
-
80051923523
-
Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins
-
Goncearenco, A. and Berezovsky, I. N. (2011) Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins. Bioinformatics, 27, 2368-2375.
-
(2011)
Bioinformatics
, vol.27
, pp. 2368-2375
-
-
Goncearenco, A.1
Berezovsky, I.N.2
-
22
-
-
84938693641
-
Diversity of c-di-GMP-binding proteins and mechanisms
-
26148715 Epub ahead of print pii: JB.00424-15
-
Chou, S. H. and Galperin, M. Y. (2015) Diversity of c-di-GMP-binding proteins and mechanisms. J. Bacteriol., pii: JB.00424-15, PMID: 26148715 (Epub ahead of print).
-
(2015)
J. Bacteriol.
-
-
Chou, S.H.1
Galperin, M.Y.2
-
23
-
-
84884281461
-
Bacterial second messengers, cGMP and c-di-GMP, in a quest for regulatory dominance
-
Gomelsky, M. and Galperin, M. Y. (2013) Bacterial second messengers, cGMP and c-di-GMP, in a quest for regulatory dominance. EMBO J., 32, 2421-2423.
-
(2013)
EMBO J.
, vol.32
, pp. 2421-2423
-
-
Gomelsky, M.1
Galperin, M.Y.2
-
25
-
-
0033972919
-
Closed loops of nearly standard size: Common basic element of protein structure
-
Berezovsky, I. N., Grosberg, A. Y. and Trifonov, E. N. (2000) Closed loops of nearly standard size: common basic element of protein structure. FEBS Lett., 466, 283-286.
-
(2000)
FEBS Lett.
, vol.466
, pp. 283-286
-
-
Berezovsky, I.N.1
Grosberg, A.Y.2
Trifonov, E.N.3
-
26
-
-
0035853276
-
Van der Waals locks: Loop-n-lock structure of globular proteins
-
Berezovsky, I. N. and Trifonov, E. N. (2001) Van der Waals locks: loop-n-lock structure of globular proteins. J. Mol. Biol., 307, 1419-1426.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 1419-1426
-
-
Berezovsky, I.N.1
Trifonov, E.N.2
-
27
-
-
84861556597
-
Exploring the evolution of protein function in Archaea
-
Goncearenco, A. and Berezovsky, I. N. (2012) Exploring the evolution of protein function in Archaea. BMC Evol. Biol., 12, 75.
-
(2012)
BMC Evol. Biol.
, vol.12
, pp. 75
-
-
Goncearenco, A.1
Berezovsky, I.N.2
-
28
-
-
84855290528
-
Divergence and convergence in enzyme evolution
-
Galperin, M. Y. and Koonin, E. V. (2012) Divergence and convergence in enzyme evolution. J. Biol. Chem., 287, 21-28.
-
(2012)
J. Biol. Chem.
, vol.287
, pp. 21-28
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
29
-
-
84941067064
-
Expanded microbial genome coverage and improved protein family annotation in the COG database
-
Galperin, M. Y., Makarova, K. S., Wolf, Y. I. and Koonin, E. V. (2015) Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res., 43, D261-D269.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D261-D269
-
-
Galperin, M.Y.1
Makarova, K.S.2
Wolf, Y.I.3
Koonin, E.V.4
-
30
-
-
52049125699
-
Origins and evolution of modern biochemistry: Insights from genomes and molecular structure
-
Caetano-Anolles, G., Sun, F. J., Wang, M., Yafremava, L. S., Harish, A., Kim, H. S., Knudsen, V., Caetano-Anolles, D. and Mittenthal, J. E. (2008) Origins and evolution of modern biochemistry: insights from genomes and molecular structure. Front. Biosci., 13, 5212-5240.
-
(2008)
Front. Biosci.
, vol.13
, pp. 5212-5240
-
-
Caetano-Anolles, G.1
Sun, F.J.2
Wang, M.3
Yafremava, L.S.4
Harish, A.5
Kim, H.S.6
Knudsen, V.7
Caetano-Anolles, D.8
Mittenthal, J.E.9
-
31
-
-
56949085134
-
The origin and evolution of modern metabolism
-
Caetano-Anolles, G., Yafremava, L. S., Gee, H., Caetano-Anolles, D., Kim, H. S. and Mittenthal, J. E. (2009) The origin and evolution of modern metabolism. Int. J. Biochem. Cell Biol., 41, 285-297.
-
(2009)
Int. J. Biochem. Cell Biol.
, vol.41
, pp. 285-297
-
-
Caetano-Anolles, G.1
Yafremava, L.S.2
Gee, H.3
Caetano-Anolles, D.4
Kim, H.S.5
Mittenthal, J.E.6
-
32
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin, A. G., Brenner, S. E., Hubbard, T. and Chothia, C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
33
-
-
0030333470
-
Three-dimensional hydrogen-bond geometry and probability information from a crystal survey
-
Mills, J. E. and Dean, P. M. (1996) Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. J. Compute Aided Mol. Des., 10, 607-622.
-
(1996)
J. Compute Aided Mol. Des.
, vol.10
, pp. 607-622
-
-
Mills, J.E.1
Dean, P.M.2
-
34
-
-
58149203231
-
InterPro: The integrative protein signature database
-
Hunter, S., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Das, U., Daugherty, L., Duquenne, L. et al. (2009) InterPro: the integrative protein signature database. Nucleic Acids Res., 37, D211-D215.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D211-D215
-
-
Hunter, S.1
Apweiler, R.2
Attwood, T.K.3
Bairoch, A.4
Bateman, A.5
Binns, D.6
Bork, P.7
Das, U.8
Daugherty, L.9
Duquenne, L.10
-
35
-
-
2142738304
-
WebLogo: A sequence logo generator
-
Crooks, G. E., Hon, G., Chandonia, J. M. and Brenner, S. E. (2004) WebLogo: a sequence logo generator. Genome Res., 14, 1188-1190.
-
(2004)
Genome Res.
, vol.14
, pp. 1188-1190
-
-
Crooks, G.E.1
Hon, G.2
Chandonia, J.M.3
Brenner, S.E.4
-
36
-
-
51049104888
-
From modeling to medicinal chemistry: Automatic generation of two-dimensional complex diagrams
-
Stierand, K. and Rarey, M. (2007) From modeling to medicinal chemistry: automatic generation of two-dimensional complex diagrams. ChemMedChem, 2, 853-860.
-
(2007)
ChemMedChem
, vol.2
, pp. 853-860
-
-
Stierand, K.1
Rarey, M.2
|