-
1
-
-
50849114838
-
Arrangements in the modular evolution of proteins
-
Moore AD, Björklund AK, Ekman D, Bornberg-Bauer E, Elofsson A. Arrangements in the modular evolution of proteins. Trends Biochem Sci. 2008; 33(9):444-51.
-
(2008)
Trends Biochem Sci.
, vol.33
, Issue.9
, pp. 444-451
-
-
Moore, A.D.1
Björklund, A.K.2
Ekman, D.3
Bornberg-Bauer, E.4
Elofsson, A.5
-
2
-
-
77958156358
-
How do proteins gain new domains?
-
Marsh JA, Teichmann SA. How do proteins gain new domains?Genome Biol. 2010; 11(7):126.
-
(2010)
Genome Biol.
, vol.11
, Issue.7
, pp. 126
-
-
Marsh, J.A.1
Teichmann, S.A.2
-
4
-
-
84879172714
-
Dynamics and adaptive benefits of modular protein evolution
-
Bornberg-Bauer E, Albà M M. Dynamics and adaptive benefits of modular protein evolution. Curr Opin Struct Biol. 2013; 23(3):459-66.
-
(2013)
Curr Opin Struct Biol.
, vol.23
, Issue.3
, pp. 459-466
-
-
Bornberg-Bauer, E.1
-
5
-
-
84858077472
-
The Pfam protein families database
-
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate JG, Boursnell C, et al. The Pfam protein families database. Nucleic Acids Res. 2012; 40(Database-Issue):290-301.
-
(2012)
Nucleic Acids Res.
, vol.40
, Issue.DATABASE ISSUE
, pp. 290-301
-
-
Punta, M.1
Coggill, P.C.2
Eberhardt, R.Y.3
Mistry, J.4
Tate, J.G.5
Boursnell, C.6
-
6
-
-
16244423379
-
Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions
-
Ekman D, Björklund AK, Frey-Skött J, Elofsson A. Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. J Mol Biol. 2005; 348(1):231-43.
-
(2005)
J Mol Biol.
, vol.348
, Issue.1
, pp. 231-243
-
-
Ekman, D.1
Björklund, A.K.2
Frey-Skött, J.3
Elofsson, A.4
-
7
-
-
67650497792
-
Nature of the protein universe
-
Levitt M. Nature of the protein universe. Proc Natl Acad Sci U S A. 2009; 106(27):11079-84.
-
(2009)
Proc Natl Acad Sci U S A.
, vol.106
, Issue.27
, pp. 11079-11084
-
-
Levitt, M.1
-
8
-
-
84861434537
-
Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution
-
Kersting AR, Bornberg-Bauer E, Moore AD, Grath S. Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution. Genome Biol Evol. 2012; 4(3):316-29.
-
(2012)
Genome Biol Evol.
, vol.4
, Issue.3
, pp. 316-329
-
-
Kersting, A.R.1
Bornberg-Bauer, E.2
Moore, A.D.3
Grath, S.4
-
9
-
-
68149147505
-
Domain shuffling and the evolution of vertebrates
-
Kawashima T, Kawashima S, Tanaka C, Murai M, Yoneda M, Putnam NH, et al. Domain shuffling and the evolution of vertebrates. Genome Res. 2009; 19(8):1393-403.
-
(2009)
Genome Res.
, vol.19
, Issue.8
, pp. 1393-1403
-
-
Kawashima, T.1
Kawashima, S.2
Tanaka, C.3
Murai, M.4
Yoneda, M.5
Putnam, N.H.6
-
10
-
-
84873192706
-
Repeated evolution of identical domain architecture in metazoan netrin domain-containing proteins
-
Leclère L, Rentzsch F. Repeated evolution of identical domain architecture in metazoan netrin domain-containing proteins. Genome Biol Evol. 2012; 4(9):883-99.
-
(2012)
Genome Biol Evol.
, vol.4
, Issue.9
, pp. 883-899
-
-
Leclère, L.1
Rentzsch, F.2
-
11
-
-
84879668651
-
A daily-updated tree of (sequenced) life as a reference for genome research
-
Fang H, Oates ME, Pethica RB, Greenwood JM, Sardar AJ, Rackham OJL, et al. A daily-updated tree of (sequenced) life as a reference for genome research. Sci Rep. 2013; 3:2015.
-
(2013)
Sci Rep.
, vol.3
, pp. 2015
-
-
Fang, H.1
Oates, M.E.2
Pethica, R.B.3
Greenwood, J.M.4
Sardar, A.J.5
Rackham, O.J.L.6
-
12
-
-
84861139508
-
Evolution of the multi-domain structures of virulence genes in the human malaria parasite, Plasmodium falciparum
-
Buckee CO, Recker M. Evolution of the multi-domain structures of virulence genes in the human malaria parasite, Plasmodium falciparum. PLoS Comput Biol. 2012; 8(4):1002451.
-
(2012)
PLoS Comput Biol.
, vol.8
, Issue.4
, pp. 1002451
-
-
Buckee, C.O.1
Recker, M.2
-
13
-
-
0348047325
-
Structure, diversity, and evolution of protein toxins from spore-forming entomopathogenic bacteria
-
de Maagd RA, Bravo A, Berry C, Crickmore N, Schnepf HE. Structure, diversity, and evolution of protein toxins from spore-forming entomopathogenic bacteria. Annu Rev Genet. 2003; 37:409-33.
-
(2003)
Annu Rev Genet.
, vol.37
, pp. 409-433
-
-
de Maagd, R.A.1
Bravo, A.2
Berry, C.3
Crickmore, N.4
Schnepf, H.E.5
-
14
-
-
0034623005
-
T-Coffee: a novel method for fast and accurate multiple sequence alignment
-
Notredame C, Higgins DG, Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000; 302(2):205-17.
-
(2000)
J Mol Biol.
, vol.302
, Issue.2
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
15
-
-
80054078476
-
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
-
Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011; 7:539.
-
(2011)
Mol Syst Biol.
, vol.7
, pp. 539
-
-
Sievers, F.1
Wilm, A.2
Dineen, D.3
Gibson, T.J.4
Karplus, K.5
Li, W.6
-
16
-
-
84883582879
-
DIALIGN at GOBICS-multiple sequence alignment using various sources of external information
-
Ait LA, Yamak Z, Morgenstern B. DIALIGN at GOBICS-multiple sequence alignment using various sources of external information. Nucleic Acids Res. 2013; 41:W3-7.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. W3-W7
-
-
Ait, L.A.1
Yamak, Z.2
Morgenstern, B.3
-
17
-
-
34249857539
-
COBALT: constraint-based alignment tool for multiple protein sequences
-
Papadopoulos JS, Agarwala R. COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics. 2007; 23(9):1073-79.
-
(2007)
Bioinformatics.
, vol.23
, Issue.9
, pp. 1073-1079
-
-
Papadopoulos, J.S.1
Agarwala, R.2
-
18
-
-
84892694478
-
Rapid similarity search of proteins using alignments of domain arrangements
-
Terrapon N, Weiner J, Grath S, Moore AD, Bornberg-Bauer E. Rapid similarity search of proteins using alignments of domain arrangements. Bioinformatics. 2014; 30(2):274-81.
-
(2014)
Bioinformatics.
, vol.30
, Issue.2
, pp. 274-281
-
-
Terrapon, N.1
Weiner, J.2
Grath, S.3
Moore, A.D.4
Bornberg-Bauer, E.5
-
19
-
-
33644876020
-
Pfam: clans, web tools and services
-
Finn RD, Mistry J, Schuster-Böckler B, Griffiths-Jones S, Hollich V, Lassmann T, et al. Pfam: clans, web tools and services. Nucleic Acids Res. 2006; 34:247-51.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 247-251
-
-
Finn, R.D.1
Mistry, J.2
Schuster-Böckler, B.3
Griffiths-Jones, S.4
Hollich, V.5
Lassmann, T.6
-
20
-
-
38549146894
-
The Pfam protein families database
-
Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz H-R, et al. The Pfam protein families database. Nucleic Acids Res. 2008; 36(Database issue):281-8.
-
(2008)
Nucleic Acids Res.
, vol.36
, Issue.DATABASE ISSUE
, pp. 281-288
-
-
Finn, R.D.1
Tate, J.2
Mistry, J.3
Coggill, P.C.4
Sammut, S.J.5
Hotz, H.-R.6
-
21
-
-
24644457706
-
BAliBASE 3.0: latest Developments of the Multiple Sequence Alignment Benchmark
-
Thompson JD, Koehl P, Ripp R, Poch O. BAliBASE 3.0: latest Developments of the Multiple Sequence Alignment Benchmark. Proteins. 2005; 61(1):127-36.
-
(2005)
Proteins.
, vol.61
, Issue.1
, pp. 127-136
-
-
Thompson, J.D.1
Koehl, P.2
Ripp, R.3
Poch, O.4
-
22
-
-
0030582739
-
Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments
-
Gotoh O. Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J Mol Biol. 1996; 264(4):823-38.
-
(1996)
J Mol Biol.
, vol.264
, Issue.4
, pp. 823-838
-
-
Gotoh, O.1
-
23
-
-
16344373015
-
Protein homology detection by HMM-HMM comparison
-
Söding J. Protein homology detection by HMM-HMM comparison. Bioinformatics. 2005; 21(7):951-60.
-
(2005)
Bioinformatics.
, vol.21
, Issue.7
, pp. 951-960
-
-
-
24
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A. 1992; 89(22):10915-9.
-
(1992)
Proc Natl Acad Sci U S A.
, vol.89
, Issue.22
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
26
-
-
0036796467
-
CDART: protein homology by domain architecture
-
Geer LY, Domrachev M, Lipman DJ, Bryant SH. CDART: protein homology by domain architecture. Genome Res. 2002; 12(10):1619-23.
-
(2002)
Genome Res.
, vol.12
, Issue.10
, pp. 1619-1623
-
-
Geer, L.Y.1
Domrachev, M.2
Lipman, D.J.3
Bryant, S.H.4
-
27
-
-
0024234855
-
CLUSTAL: a package for performing multiple sequence alignment on a microcomputer
-
Higgins DG, Sharp PM. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene. 1988; 73(1):237-44.
-
(1988)
Gene.
, vol.73
, Issue.1
, pp. 237-244
-
-
Higgins, D.G.1
Sharp, P.M.2
-
28
-
-
59549102237
-
Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment
-
Paten B, Herrero J, Beal K, Birney E. Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. Bioinformatics. 2008; 25(3):259-91.
-
(2008)
Bioinformatics.
, vol.25
, Issue.3
, pp. 259-291
-
-
Paten, B.1
Herrero, J.2
Beal, K.3
Birney, E.4
-
29
-
-
80055082271
-
Accelerated profile HMM searches
-
Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol. 2011; 7(10):1002195.
-
(2011)
PLoS Comput Biol.
, vol.7
, Issue.10
, pp. 1002195
-
-
Eddy, S.R.1
-
30
-
-
13744252890
-
MAFFT version 5: improvement in accuracy of multiple sequence alignment
-
Katoh K, Kuma K, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005; 33(2):511-8.
-
(2005)
Nucleic Acids Res.
, vol.33
, Issue.2
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
Miyata, T.4
|