-
1
-
-
0035182669
-
Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions
-
Afonnikov, D. A., D. Y. Oshchepkov, and N. A. Kolchanov. 2001. Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions. Bioinformatics 17:1035-1046.
-
(2001)
Bioinformatics
, vol.17
, pp. 1035-1046
-
-
Afonnikov, D.A.1
Oshchepkov, D.Y.2
Kolchanov, N.A.3
-
2
-
-
16344379182
-
Covarion structure in plastid genome evolution: A new statistical test
-
Ane, C., J. G. Burleigh, M. M. McMahon, and M. J. Sanderson. 2005. Covarion structure in plastid genome evolution: a new statistical test. Mol. Biol. Evol. 22:914-924.
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 914-924
-
-
Ane, C.1
Burleigh, J.G.2
McMahon, M.M.3
Sanderson, M.J.4
-
3
-
-
0034897644
-
Phylogenetic analyses of amino acid variation in the serpin proteins
-
Atchley, W. R., T. Lokot, K. Wollenberg, A. Dress, and H. Ragg. 2001. Phylogenetic analyses of amino acid variation in the serpin proteins. Mol. Biol. Evol. 18:1502-1511.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 1502-1511
-
-
Atchley, W.R.1
Lokot, T.2
Wollenberg, K.3
Dress, A.4
Ragg, H.5
-
4
-
-
0032925848
-
Positional dependence, cliques, and predictive motifs in the bHLH protein domain
-
Atchley, W. R., W. Terhalle, and A. Dress. 1999. Positional dependence, cliques, and predictive motifs in the bHLH protein domain. J. Mol. Evol. 48:501-516.
-
(1999)
J. Mol. Evol.
, vol.48
, pp. 501-516
-
-
Atchley, W.R.1
Terhalle, W.2
Dress, A.3
-
5
-
-
0033977832
-
Correlations among amino acid sites in bHLH protein domains: An information theoretic analysis
-
Atchley, W. R., K. R. Wollenberg, W. M. Fitch, W. Terhalle, and A. W. Dress. 2000. Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis. Mol. Biol. Evol. 17:164-178.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 164-178
-
-
Atchley, W.R.1
Wollenberg, K.R.2
Fitch, W.M.3
Terhalle, W.4
Dress, A.W.5
-
6
-
-
0033757806
-
The Protein Data Bank and the challenge of structural genomics
-
Berman, H. M., T. N. Bhat, P. E. Bourne, Z. Feng, G. Gilliland, H. Weissig, and J. Westbrook. 2000. The Protein Data Bank and the challenge of structural genomics. Nat. Struct. Biol. 7(Suppl.):957-959.
-
(2000)
Nat. Struct. Biol.
, vol.7
, Issue.SUPPL.
, pp. 957-959
-
-
Berman, H.M.1
Bhat, T.N.2
Bourne, P.E.3
Feng, Z.4
Gilliland, G.5
Weissig, H.6
Westbrook, J.7
-
7
-
-
0142095053
-
Mutation of the highly conserved tryptophan in the serpin breach region alters the inhibitory mechanism of plasminogen activator inhibitor-1
-
Blouse, G. E., M. J. Perron, J. O. Kvassman, S. Yunus, J. H. Thompson, R. L. Betts, L. C. Lutter, and J. D. Shore. 2003. Mutation of the highly conserved tryptophan in the serpin breach region alters the inhibitory mechanism of plasminogen activator inhibitor-1. Biochemistry 42:12260-12272.
-
(2003)
Biochemistry
, vol.42
, pp. 12260-12272
-
-
Blouse, G.E.1
Perron, M.J.2
Kvassman, J.O.3
Yunus, S.4
Thompson, J.H.5
Betts, R.L.6
Lutter, L.C.7
Shore, J.D.8
-
8
-
-
0030970646
-
An analysis of simultaneous variation in protein structures
-
Chelvanayagam, G., A. Eggenschwiler, L. Knecht, G. H. Gonnet, and S. A. Benner. 1997. An analysis of simultaneous variation in protein structures. Protein Eng. 10:307-316.
-
(1997)
Protein Eng.
, vol.10
, pp. 307-316
-
-
Chelvanayagam, G.1
Eggenschwiler, A.2
Knecht, L.3
Gonnet, G.H.4
Benner, S.A.5
-
9
-
-
0028832687
-
Covariation of residues in the homeodomain sequence family
-
Clarke, N. D. 1995. Covariation of residues in the homeodomain sequence family. Protein Sci. 4:2269-2278.
-
(1995)
Protein Sci.
, vol.4
, pp. 2269-2278
-
-
Clarke, N.D.1
-
10
-
-
0033598346
-
Familial dementia caused by polymerization of mutant neuroserpin
-
Davis, R. L., A. E. Shrimpton, P. D. Holohan et al. (20 co-authors). 1999. Familial dementia caused by polymerization of mutant neuroserpin. Nature 401:376-379.
-
(1999)
Nature
, vol.401
, pp. 376-379
-
-
Davis, R.L.1
Shrimpton, A.E.2
Holohan, P.D.3
-
11
-
-
1542510099
-
Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting
-
Desper, R., and O. Gascuel. 2004. Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol. Biol. Evol. 21:587-598.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 587-598
-
-
Desper, R.1
Gascuel, O.2
-
12
-
-
17744409446
-
Wild-type alpha 1-antitrypsin is in the canonical inhibitory conformation
-
Elliott, P. R., J. P. Abrahams, and D. A. Lomas. 1998. Wild-type alpha 1-antitrypsin is in the canonical inhibitory conformation. J. Mol. Biol. 275:419-425.
-
(1998)
J. Mol. Biol.
, vol.275
, pp. 419-425
-
-
Elliott, P.R.1
Abrahams, J.P.2
Lomas, D.A.3
-
13
-
-
0015162378
-
Rate of change of concomitantly variable codons
-
Fitch, W. M. 1971. Rate of change of concomitantly variable codons. J. Mol. Evol. 1:84-96.
-
(1971)
J. Mol. Evol.
, vol.1
, pp. 84-96
-
-
Fitch, W.M.1
-
14
-
-
0014860857
-
An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution
-
Fitch, W. M., and E. Markowitz. 1970. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem. Genet. 4:579-593.
-
(1970)
Biochem. Genet.
, vol.4
, pp. 579-593
-
-
Fitch, W.M.1
Markowitz, E.2
-
15
-
-
0035895207
-
Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors
-
Gaucher, E. A., M. M. Miyamoto, and S. A. Benner. 2001. Function-structure analysis of proteins using covarion-based evolutionary approaches: elongation factors. Proc. Natl. Acad. Sci. USA 98:548-552.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 548-552
-
-
Gaucher, E.A.1
Miyamoto, M.M.2
Benner, S.A.3
-
16
-
-
0037125184
-
The F-helix of serpins plays an essential, active role in the proteinase inhibition mechanism
-
Gettins, P. G. 2002a. The F-helix of serpins plays an essential, active role in the proteinase inhibition mechanism. FEBS Lett. 523:2-6.
-
(2002)
FEBS Lett.
, vol.523
, pp. 2-6
-
-
Gettins, P.G.1
-
17
-
-
0036882395
-
Serpin structure, mechanism, and function
-
-. 2002b. Serpin structure, mechanism, and function. Chem. Rev. 102:4751-4804.
-
(2002)
Chem. Rev.
, vol.102
, pp. 4751-4804
-
-
-
18
-
-
0033555456
-
The crystal structure of plasminogen activator inhibitor 2 at 2.0 A resolution: Implications for serpin function
-
Harrop, S. J., L. Jankova, M. Coles, D. Jardine, J. S. Whittaker, A. R. Gould, A. Meister, G. C. King, B. C. Mabbutt, and P. M. Curmi. 1999. The crystal structure of plasminogen activator inhibitor 2 at 2.0 A resolution: implications for serpin function. Structure Fold. Des. 7:43-54.
-
(1999)
Structure Fold. Des.
, vol.7
, pp. 43-54
-
-
Harrop, S.J.1
Jankova, L.2
Coles, M.3
Jardine, D.4
Whittaker, J.S.5
Gould, A.R.6
Meister, A.7
King, G.C.8
Mabbutt, B.C.9
Curmi, P.M.10
-
19
-
-
0027182969
-
Effects of mutations in the hinge region of serpins
-
Hopkins, P. C., R. W. Carrell, and S. R. Stone. 1993. Effects of mutations in the hinge region of serpins. Biochemistry 32:7650-7657.
-
(1993)
Biochemistry
, vol.32
, pp. 7650-7657
-
-
Hopkins, P.C.1
Carrell, R.W.2
Stone, S.R.3
-
21
-
-
3042601821
-
Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies
-
Inagaki, Y., E. Susko, N. M. Fast, and A. J. Roger. 2004. Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies. Mol. Biol. Evol. 21:1340-1349.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 1340-1349
-
-
Inagaki, Y.1
Susko, E.2
Fast, N.M.3
Roger, A.J.4
-
22
-
-
1542496192
-
The 1.5 A crystal structure of a prokaryote serpin: Controlling conformational change in a heated environment
-
Irving, J. A., L. D. Cabrita, J. Rossjohn, R. N. Pike, S. P. Bottomley, and J. C. Whisstock. 2003. The 1.5 A crystal structure of a prokaryote serpin: controlling conformational change in a heated environment. Structure (Camb.) 11:387-397.
-
(2003)
Structure (Camb.)
, vol.11
, pp. 387-397
-
-
Irving, J.A.1
Cabrita, L.D.2
Rossjohn, J.3
Pike, R.N.4
Bottomley, S.P.5
Whisstock, J.C.6
-
23
-
-
0034523345
-
Phylogeny of the serpin superfamily: Implications of patterns of amino acid conservation for structure and function
-
Irving, J. A., R. N. Pike, A. M. Lesk, and J. C. Whisstock. 2000. Phylogeny of the serpin superfamily: implications of patterns of amino acid conservation for structure and function. Genome Res. 10:1845-1864.
-
(2000)
Genome Res.
, vol.10
, pp. 1845-1864
-
-
Irving, J.A.1
Pike, R.N.2
Lesk, A.M.3
Whisstock, J.C.4
-
24
-
-
1842853550
-
Serpins in prokaryotes
-
Irving, J. A., P. J. Steenbakkers, A. M. Lesk, H. J. Op den Camp, R. N. Pike, and J. C. Whisstock. 2002. Serpins in prokaryotes. Mol. Biol. Evol. 19:1881-1890.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 1881-1890
-
-
Irving, J.A.1
Steenbakkers, P.J.2
Lesk, A.M.3
Op Den Camp, H.J.4
Pike, R.N.5
Whisstock, J.C.6
-
26
-
-
34250922831
-
The varimax criterion for analytic rotation in factor analysis
-
Kaiser, H. F. 1958. The varimax criterion for analytic rotation in factor analysis. Psychometrika 23:187-200.
-
(1958)
Psychometrika
, vol.23
, pp. 187-200
-
-
Kaiser, H.F.1
-
28
-
-
0027297096
-
Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: An information theoretic analysis
-
Korber, B. T., R. M. Farber, D. H. Wolpert, and A. S. Lapedes. 1993. Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis. Proc. Natl. Acad. Sci. USA 90:7176-7180.
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 7176-7180
-
-
Korber, B.T.1
Farber, R.M.2
Wolpert, D.H.3
Lapedes, A.S.4
-
29
-
-
0141509877
-
Conserved Ser residues, the shutter region, and speciation in serpin evolution
-
Krem, M. M., and E. Di Cera. 2003. Conserved Ser residues, the shutter region, and speciation in serpin evolution. J. Biol. Chem. 278:37810-37814.
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 37810-37814
-
-
Krem, M.M.1
Di Cera, E.2
-
30
-
-
0015222647
-
The interpretation of protein structures: Estimation of static accessibility
-
Lee, B., and F. M. Richards. 1971. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:379-400.
-
(1971)
J. Mol. Biol.
, vol.55
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
-
31
-
-
0035964912
-
Role of the connectivity of secondary structure segments in the folding of alpha(1)-antitrypsin
-
Lee, C., E. I. Seo, and M. H. Yu. 2001. Role of the connectivity of secondary structure segments in the folding of alpha(1)-antitrypsin. Biochem. Biophys. Res. Commun. 287:636-641.
-
(2001)
Biochem. Biophys. Res. Commun.
, vol.287
, pp. 636-641
-
-
Lee, C.1
Seo, E.I.2
Yu, M.H.3
-
32
-
-
0021747157
-
Human alpha 1-proteinase inhibitor. Crystal structure analysis of two crystal modifications, molecular model and preliminary analysis of the implications for function
-
Loebermann, H., R. Tokuoka, I. Deisenhofer, and R. Huber. 1984. Human alpha 1-proteinase inhibitor. Crystal structure analysis of two crystal modifications, molecular model and preliminary analysis of the implications for function. J. Mol. Biol. 177:531-557.
-
(1984)
J. Mol. Biol.
, vol.177
, pp. 531-557
-
-
Loebermann, H.1
Tokuoka, R.2
Deisenhofer, I.3
Huber, R.4
-
33
-
-
0028941449
-
Preparation and characterization of latent alpha 1-antitrypsin
-
Lomas, D. A., P. R. Elliott, W. S. Chang, M. R. Wardell, andR. W. Carrell. 1995. Preparation and characterization of latent alpha 1-antitrypsin. J. Biol. Chem. 270:5282-5288.
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 5282-5288
-
-
Lomas, D.A.1
Elliott, P.R.2
Chang, W.S.3
Wardell, M.R.4
Carrell, R.W.5
-
34
-
-
0026546881
-
Structural basis of latency in plasminogen activator inhibitor-1
-
Mottonen, I., A. Strand, I. Symersky, R. M. Sweet, D. E. Danley, K. F. Geoghegan, R. D. Gerard, and E. I. Goldsmith. 1992. Structural basis of latency in plasminogen activator inhibitor-1. Nature 355:270-273.
-
(1992)
Nature
, vol.355
, pp. 270-273
-
-
Mottonen, I.1
Strand, A.2
Symersky, I.3
Sweet, R.M.4
Danley, D.E.5
Geoghegan, K.F.6
Gerard, R.D.7
Goldsmith, E.I.8
-
35
-
-
0030743758
-
Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution
-
Pollock, D. D., and W. R. Taylor. 1997. Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Eng. 10:647-657.
-
(1997)
Protein Eng.
, vol.10
, pp. 647-657
-
-
Pollock, D.D.1
Taylor, W.R.2
-
36
-
-
0033582946
-
Coevolving protein residues: Maximum likelihood identification and relationship to structure
-
Pollock, D. D., W. R. Taylor, and N. Goldman. 1999. Coevolving protein residues: maximum likelihood identification and relationship to structure. J. Mol. Biol. 287:187-198.
-
(1999)
J. Mol. Biol.
, vol.287
, pp. 187-198
-
-
Pollock, D.D.1
Taylor, W.R.2
Goldman, N.3
-
37
-
-
0034794239
-
Evaluation of a novel method for the identification of coevolving protein residues
-
Pritchard, L., P. Bladon, I. M. O. Mitchell, and M. I. Dufton. 2001. Evaluation of a novel method for the identification of coevolving protein residues. Protein Eng. 14:549-555.
-
(2001)
Protein Eng.
, vol.14
, pp. 549-555
-
-
Pritchard, L.1
Bladon, P.2
Mitchell, I.M.O.3
Dufton, M.I.4
-
38
-
-
0002218484
-
Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
-
Pupko, T., R. E. Bell, I. Mayrose, F. Glaser, and N. Ben-Tal. 2002. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18 (Suppl. 1):S71-S77.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Pupko, T.1
Bell, R.E.2
Mayrose, I.3
Glaser, F.4
Ben-Tal, N.5
-
39
-
-
0035060052
-
Vertebrate serpins: Construction of a conflict-free phytogeny by combining exon-intron and diagnostic site analyses
-
Ragg, H., T. Lokot, P. B. Kamp, W. R. Atchley, and A. Dress. 2001. Vertebrate serpins: construction of a conflict-free phytogeny by combining exon-intron and diagnostic site analyses. Mol. Biol. Evol. 18:577-584.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 577-584
-
-
Ragg, H.1
Lokot, T.2
Kamp, P.B.3
Atchley, W.R.4
Dress, A.5
-
40
-
-
4644325614
-
Serpins in unicellular Eukarya, Archaea, and Bacteria: Sequence analysis and evolution
-
Roberts, T. H., J. Hejgaard, N. F. Saunders, R. Cavicchioli, and P. M. Curmi. 2004. Serpins in unicellular Eukarya, Archaea, and Bacteria: sequence analysis and evolution. J. Mol. Evol. 59:437-447.
-
(2004)
J. Mol. Evol.
, vol.59
, pp. 437-447
-
-
Roberts, T.H.1
Hejgaard, J.2
Saunders, N.F.3
Cavicchioli, R.4
Curmi, P.M.5
-
42
-
-
0029589824
-
What do dysfunctional serpins tell us about molecular mobility and disease?
-
Stein, P. E., and R. W. Carrell. 1995. What do dysfunctional serpins tell us about molecular mobility and disease? Nat. Struct. Biol. 2:96-113.
-
(1995)
Nat. Struct. Biol.
, vol.2
, pp. 96-113
-
-
Stein, P.E.1
Carrell, R.W.2
-
43
-
-
0033744204
-
Exploring a phylogenetic approach for the detection of correlated substitutions in proteins
-
Tuff, P., and P. Darlu. 2000. Exploring a phylogenetic approach for the detection of correlated substitutions in proteins. Mol. Biol. Evol. 17:1753-1759.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 1753-1759
-
-
Tuff, P.1
Darlu, P.2
-
44
-
-
19944406094
-
Context dependence and coevolution among amino acid residues in proteins
-
Wang, Z. O. and D. D. Pollock. 2005. Context dependence and coevolution among amino acid residues in proteins. Methods Enzmol. 395:779-790.
-
(2005)
Methods Enzmol.
, vol.395
, pp. 779-790
-
-
Wang, Z.O.1
Pollock, D.D.2
-
45
-
-
0034695402
-
Conformational changes in serpins: I. The native and cleaved conformations of alpha(1)-antitrypsin
-
Whisstock, J. C., R. Skinner, R. W. Carrell, and A. M. Lesk. 2000. Conformational changes in serpins: I. The native and cleaved conformations of alpha(1)-antitrypsin. J. Mol. Biol. 295:651-665.
-
(2000)
J. Mol. Biol.
, vol.295
, pp. 651-665
-
-
Whisstock, J.C.1
Skinner, R.2
Carrell, R.W.3
Lesk, A.M.4
|