-
1
-
-
84941039390
-
CATH: comprehensive structural and functional annotations for genome sequences
-
Sillitoe I., Lewis T.E., Cuff A., Das S., Ashford P., Dawson N.L., Furnham N., Laskowski R.A., Lee D., Lees J.G., et al. CATH: comprehensive structural and functional annotations for genome sequences. Nucleic Acids Res 2015, 43:D376-D381.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. D376-D381
-
-
Sillitoe, I.1
Lewis, T.E.2
Cuff, A.3
Das, S.4
Ashford, P.5
Dawson, N.L.6
Furnham, N.7
Laskowski, R.A.8
Lee, D.9
Lees, J.G.10
-
2
-
-
84976865403
-
The Pfam protein families database: towards a more sustainable future
-
Finn R.D., Coggill P., Eberhardt R.Y., Eddy S.R., Mistry J., Mitchell A.L., Potter S.C., Punta M., Qureshi M., Sangrador-Vegas A., et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 2015, 44:D279-D285.
-
(2015)
Nucleic Acids Res
, vol.44
, pp. D279-D285
-
-
Finn, R.D.1
Coggill, P.2
Eberhardt, R.Y.3
Eddy, S.R.4
Mistry, J.5
Mitchell, A.L.6
Potter, S.C.7
Punta, M.8
Qureshi, M.9
Sangrador-Vegas, A.10
-
3
-
-
0028961335
-
SCOP: a structural classification of proteins database for the investigation of sequences and structures
-
Murzin A.G., Brenner S.E., Hubbard T., Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 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
-
4
-
-
84891783706
-
SCOP2 prototype: a new approach to protein structure mining
-
Andreeva A., Howorth D., Chothia C., Kulesha E., Murzin A.G. SCOP2 prototype: a new approach to protein structure mining. Nucleic Acids Res 2014, 42.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Andreeva, A.1
Howorth, D.2
Chothia, C.3
Kulesha, E.4
Murzin, A.G.5
-
5
-
-
84943516185
-
Structural bridges through fold space
-
Edwards H., Deane C.M. Structural bridges through fold space. PLoS Comput Biol 2015, 11:e1004466.
-
(2015)
PLoS Comput Biol
, vol.11
, pp. e1004466
-
-
Edwards, H.1
Deane, C.M.2
-
6
-
-
80055082271
-
Accelerated profile HMM searches
-
Eddy S.R. Accelerated profile HMM searches. PLoS Comput Biol 2011, 7.
-
(2011)
PLoS Comput Biol
, vol.7
-
-
Eddy, S.R.1
-
7
-
-
84976904331
-
Gene3D: expanding the utility of domain assignments
-
Lam S.D., Dawson N.L., Das S., Sillitoe I., Ashford P., Lee D., Lehtinen S., Orengo C.A., Lees J.G. Gene3D: expanding the utility of domain assignments. Nucleic Acids Res 2015, 44:D404-D409.
-
(2015)
Nucleic Acids Res
, vol.44
, pp. D404-D409
-
-
Lam, S.D.1
Dawson, N.L.2
Das, S.3
Sillitoe, I.4
Ashford, P.5
Lee, D.6
Lehtinen, S.7
Orengo, C.A.8
Lees, J.G.9
-
8
-
-
84941032473
-
The SUPERFAMILY 1.75 database in 2014: a doubling of data
-
Oates M.E., Stahlhacke J., Vavoulis D.V., Smithers B., Rackham O.J.L., Sardar A.J., Zaucha J., Thurlby N., Fang H., Gough J. The SUPERFAMILY 1.75 database in 2014: a doubling of data. Nucleic Acids Res 2015, 43:D227-D233.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. D227-D233
-
-
Oates, M.E.1
Stahlhacke, J.2
Vavoulis, D.V.3
Smithers, B.4
Rackham, O.J.L.5
Sardar, A.J.6
Zaucha, J.7
Thurlby, N.8
Fang, H.9
Gough, J.10
-
9
-
-
84947605491
-
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation
-
Das S., Lee D., Sillitoe I., Dawson N.L., Lees J.G., Orengo C.A. Functional classification of CATH superfamilies: a domain-based approach for protein function annotation. Bioinformatics 2014, 31:3460-3467.
-
(2014)
Bioinformatics
, vol.31
, pp. 3460-3467
-
-
Das, S.1
Lee, D.2
Sillitoe, I.3
Dawson, N.L.4
Lees, J.G.5
Orengo, C.A.6
-
11
-
-
84874663959
-
A large-scale evaluation of computational protein function prediction
-
Radivojac P., Clark W.T., Oron T.R., Schnoes A.M., Wittkop T., Sokolov A., Graim K., Funk C., Verspoor K., Ben-Hur A., et al. A large-scale evaluation of computational protein function prediction. Nat Methods 2013, 10:221-227.
-
(2013)
Nat Methods
, vol.10
, pp. 221-227
-
-
Radivojac, P.1
Clark, W.T.2
Oron, T.R.3
Schnoes, A.M.4
Wittkop, T.5
Sokolov, A.6
Graim, K.7
Funk, C.8
Verspoor, K.9
Ben-Hur, A.10
-
12
-
-
84986207718
-
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
-
Jiang Y., Oron T.R., Clark W.T., Bankapur A.R., D'Andrea D., Lepore R., Funk C.S., Kahanda I., Verspoor K.M., Ben-Hur A., et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy 2016, arxiv, http://arxiv.org/abs/1601.00891.
-
(1983)
Genome Biology
, vol.17
, Issue.1
-
-
Jiang, Y.1
Oron, T.R.2
Clark , W.T.3
Bankapur , A.R.4
-
13
-
-
84925114160
-
Intrinsically disordered proteins in cellular signalling and regulation
-
Wright P.E., Dyson H.J. Intrinsically disordered proteins in cellular signalling and regulation. Nat Rev Mol Cell Biol 2014, 16:18-29.
-
(2014)
Nat Rev Mol Cell Biol
, vol.16
, pp. 18-29
-
-
Wright, P.E.1
Dyson, H.J.2
-
14
-
-
79851508882
-
Bringing order to protein disorder through comparative genomics and genetic interactions
-
Bellay J., Han S., Michaut M., Kim T., Costanzo M., Andrews B.J., Boone C., Bader G.D., Myers C.L., Kim P.M. Bringing order to protein disorder through comparative genomics and genetic interactions. Genome Biol 2011, 12:R14.
-
(2011)
Genome Biol
, vol.12
, pp. R14
-
-
Bellay, J.1
Han, S.2
Michaut, M.3
Kim, T.4
Costanzo, M.5
Andrews, B.J.6
Boone, C.7
Bader, G.D.8
Myers, C.L.9
Kim, P.M.10
-
16
-
-
0035815113
-
Evolution of function in protein superfamilies, from a structural perspective
-
Todd A.E., Orengo C.a., Thornton J.M. Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol 2001, 307:1113-1143.
-
(2001)
J Mol Biol
, vol.307
, pp. 1113-1143
-
-
Todd, A.E.1
Orengo, C.2
Thornton, J.M.3
-
17
-
-
33846059668
-
The generation of new protein functions by the combination of domains
-
Bashton M., Chothia C. The generation of new protein functions by the combination of domains. Structure 2007, 15:85-99.
-
(2007)
Structure
, vol.15
, pp. 85-99
-
-
Bashton, M.1
Chothia, C.2
-
18
-
-
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, 23:459-466.
-
(2013)
Curr Opin Struct Biol
, vol.23
, pp. 459-466
-
-
Bornberg-Bauer, E.1
Albà, M.M.2
-
19
-
-
84943575068
-
The language of the protein universe
-
Scaiewicz A., Levitt M. The language of the protein universe. Curr Opin Genet Dev 2015, 35:50-56.
-
(2015)
Curr Opin Genet Dev
, vol.35
, pp. 50-56
-
-
Scaiewicz, A.1
Levitt, M.2
-
20
-
-
0842268045
-
Supra-domains: evolutionary units larger than single protein domains
-
Vogel C., Berzuini C., Bashton M., Gough J., Teichmann S.A. Supra-domains: evolutionary units larger than single protein domains. J Mol Biol 2004, 336:809-823.
-
(2004)
J Mol Biol
, vol.336
, pp. 809-823
-
-
Vogel, C.1
Berzuini, C.2
Bashton, M.3
Gough, J.4
Teichmann, S.A.5
-
21
-
-
0017771466
-
Evolution and tinkering
-
Jacob F. Evolution and tinkering. Science 1977, 196:1161-1166.
-
(1977)
Science
, vol.196
, pp. 1161-1166
-
-
Jacob, F.1
-
23
-
-
84876083730
-
A reference transcriptome and inferred proteome for the salamander Notophthalmus viridescens
-
Abdullayev I., Kirkham M., Björklund Å.K., Simon A., Sandberg R. A reference transcriptome and inferred proteome for the salamander Notophthalmus viridescens. Exp Cell Res 2013, 319:1187-1197.
-
(2013)
Exp Cell Res
, vol.319
, pp. 1187-1197
-
-
Abdullayev, I.1
Kirkham, M.2
Björklund Å, K.3
Simon, A.4
Sandberg, R.5
-
24
-
-
84871832159
-
The complex NOD-like receptor repertoire of the coral acropora digitifera includes novel domain combinations
-
Hamada M., Shoguchi E., Shinzato C., Kawashima T., Miller D.J., Satoh N. The complex NOD-like receptor repertoire of the coral acropora digitifera includes novel domain combinations. Mol Biol Evol 2013, 30:167-176.
-
(2013)
Mol Biol Evol
, vol.30
, pp. 167-176
-
-
Hamada, M.1
Shoguchi, E.2
Shinzato, C.3
Kawashima, T.4
Miller, D.J.5
Satoh, N.6
-
25
-
-
84970016768
-
Proteins with highly evolvable domain architectures are nonessential but highly retained
-
Hsu C.-H., Chiang A.W.T., Hwang M.-J., Liao B.-Y. Proteins with highly evolvable domain architectures are nonessential but highly retained. Mol Biol Evol 2016, 10.1093/molbev/msw006.
-
(2016)
Mol Biol Evol
-
-
Hsu, C.-H.1
Chiang, A.W.T.2
Hwang, M.-J.3
Liao, B.-Y.4
-
26
-
-
79951662075
-
Evolution of domain promiscuity in eukaryotic genomes - a perspective from the inferred ancestral domain architectures
-
Cohen-Gihon I., Fong J.H., Sharan R., Nussinov R., Przytycka T.M., Panchenko A.R. Evolution of domain promiscuity in eukaryotic genomes - a perspective from the inferred ancestral domain architectures. Mol Biosyst 2011, 7:784-792.
-
(2011)
Mol Biosyst
, vol.7
, pp. 784-792
-
-
Cohen-Gihon, I.1
Fong, J.H.2
Sharan, R.3
Nussinov, R.4
Przytycka, T.M.5
Panchenko, A.R.6
-
27
-
-
84860664619
-
-
Springer Science & Business Media
-
Introduction to Marine Genomics 2010, Springer Science & Business Media.
-
(2010)
Introduction to Marine Genomics
-
-
-
28
-
-
84901457312
-
The evolution of human cells in terms of protein innovation
-
Sardar A.J., Oates M.E., Fang H., Forrest A.R.R., Kawaji H., Gough J., Rackham O.J.L. The evolution of human cells in terms of protein innovation. Mol Biol Evol 2014, 31:1364-1374.
-
(2014)
Mol Biol Evol
, vol.31
, pp. 1364-1374
-
-
Sardar, A.J.1
Oates, M.E.2
Fang, H.3
Forrest, A.R.R.4
Kawaji, H.5
Gough, J.6
Rackham, O.J.L.7
-
29
-
-
84955379926
-
Causes of evolutionary rate variation among protein sites
-
Echave J., Spielman S.J., Wilke C.O. Causes of evolutionary rate variation among protein sites. Nat Rev Genet 2016, 17:109-121.
-
(2016)
Nat Rev Genet
, vol.17
, pp. 109-121
-
-
Echave, J.1
Spielman, S.J.2
Wilke, C.O.3
-
30
-
-
84954366001
-
The TIM barrel architecture facilitated the early evolution of protein-mediated metabolism
-
Goldman A.D., Beatty J.T., Landweber L.F. The TIM barrel architecture facilitated the early evolution of protein-mediated metabolism. J Mol Evol 2016, 82:1-10.
-
(2016)
J Mol Evol
, vol.82
, pp. 1-10
-
-
Goldman, A.D.1
Beatty, J.T.2
Landweber, L.F.3
-
31
-
-
84957449877
-
Large-scale analysis exploring evolution of catalytic machineries and mechanisms in enzyme superfamilies
-
Furnham N., Dawson N.L., Rahman S.A., Thornton J.M., Orengo C.A. Large-scale analysis exploring evolution of catalytic machineries and mechanisms in enzyme superfamilies. J Mol Biol 2015, 428:253-267.
-
(2015)
J Mol Biol
, vol.428
, pp. 253-267
-
-
Furnham, N.1
Dawson, N.L.2
Rahman, S.A.3
Thornton, J.M.4
Orengo, C.A.5
-
32
-
-
84908587486
-
New insights about enzyme evolution from large-scale studies of sequence and structure relationships
-
Brown S.D., Babbitt P.C. New insights about enzyme evolution from large-scale studies of sequence and structure relationships. J Biol Chem 2014, 10.1074/jbc.R114.569350.
-
(2014)
J Biol Chem
-
-
Brown, S.D.1
Babbitt, P.C.2
-
33
-
-
84876286975
-
Functional site plasticity in domain superfamilies
-
Dessailly B.H., Dawson N.L., Mizuguchi K., Orengo C.A. Functional site plasticity in domain superfamilies. Biochim Biophys Acta - Proteins Proteomics 2013, 1834:874-889.
-
(2013)
Biochim Biophys Acta - Proteins Proteomics
, vol.1834
, pp. 874-889
-
-
Dessailly, B.H.1
Dawson, N.L.2
Mizuguchi, K.3
Orengo, C.A.4
-
34
-
-
84879549646
-
What makes a protein fold amenable to functional innovation? Fold polarity and stability trade-offs
-
Dellus-Gur E., Toth-Petroczy A., Elias M., Tawfik D.S. What makes a protein fold amenable to functional innovation? Fold polarity and stability trade-offs. J Mol Biol 2013, 425:2609-2621.
-
(2013)
J Mol Biol
, vol.425
, pp. 2609-2621
-
-
Dellus-Gur, E.1
Toth-Petroczy, A.2
Elias, M.3
Tawfik, D.S.4
-
35
-
-
84904416740
-
The robustness and innovability of protein folds
-
Toth-Petroczy A., Tawfik D.S. The robustness and innovability of protein folds. Curr Opin Struct Biol 2014, 26:131-138.
-
(2014)
Curr Opin Struct Biol
, vol.26
, pp. 131-138
-
-
Toth-Petroczy, A.1
Tawfik, D.S.2
-
36
-
-
84893867514
-
Stability-activity tradeoffs constrain the adaptive evolution of RubisCO
-
Studer R.A., Christin P.-A., Williams M.A., Orengo C. Stability-activity tradeoffs constrain the adaptive evolution of RubisCO. Proc Natl Acad Sci U S A 2014, 111:2223-2228.
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, pp. 2223-2228
-
-
Studer, R.A.1
Christin, P.-A.2
Williams, M.A.3
Orengo, C.4
-
37
-
-
78149272906
-
Robustness and evolvability in the functional anatomy of a PER-ARNT-SIM (PAS) domain
-
Philip A.F., Kumauchi M., Hoff W.D. Robustness and evolvability in the functional anatomy of a PER-ARNT-SIM (PAS) domain. Proc Natl Acad Sci U S A 2010, 107:17986-17991.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 17986-17991
-
-
Philip, A.F.1
Kumauchi, M.2
Hoff, W.D.3
-
38
-
-
84971655027
-
Functional sites induce long-range evolutionary constraints in enzymes
-
Jack B.R., Meyer A.G., Echave J., Wilke C.O. Functional sites induce long-range evolutionary constraints in enzymes. PLOS Biol 2016, 14:e1002452.
-
(2016)
PLOS Biol
, vol.14
, pp. e1002452
-
-
Jack, B.R.1
Meyer, A.G.2
Echave, J.3
Wilke, C.O.4
-
39
-
-
84956891086
-
Evolution of an ancient protein function involved in organized multicellularity in animals
-
Anderson D.P., Whitney D.S., Hanson-Smith V., Woznica A., Campodonico-Burnett W., Volkman B.F., King N., Prehoda K.E., Thornton J.W. Evolution of an ancient protein function involved in organized multicellularity in animals. Elife 2016, 5:1-21.
-
(2016)
Elife
, vol.5
, pp. 1-21
-
-
Anderson, D.P.1
Whitney, D.S.2
Hanson-Smith, V.3
Woznica, A.4
Campodonico-Burnett, W.5
Volkman, B.F.6
King, N.7
Prehoda, K.E.8
Thornton, J.W.9
-
40
-
-
84902526453
-
Resilience of biochemical activity in protein domains in the face of structural divergence
-
Zhang D., Iyer L.M., Burroughs A.M., Aravind L. Resilience of biochemical activity in protein domains in the face of structural divergence. Curr Opin Struct Biol 2014, 26:92-103.
-
(2014)
Curr Opin Struct Biol
, vol.26
, pp. 92-103
-
-
Zhang, D.1
Iyer, L.M.2
Burroughs, A.M.3
Aravind, L.4
-
41
-
-
78651412161
-
Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires
-
Zmasek C.M., Godzik A. Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires. Genome Biol 2011, 12:R4.
-
(2011)
Genome Biol
, vol.12
, pp. R4
-
-
Zmasek, C.M.1
Godzik, A.2
-
42
-
-
84881612486
-
Genome reduction as the dominant mode of evolution
-
Wolf Y.I., Koonin E.V. Genome reduction as the dominant mode of evolution. BioEssays 2013, 35:829-837.
-
(2013)
BioEssays
, vol.35
, pp. 829-837
-
-
Wolf, Y.I.1
Koonin, E.V.2
-
44
-
-
77958156358
-
How do proteins gain new domains?
-
Marsh J.A., Teichmann S.A. How do proteins gain new domains?. Genome Biol 2010, 11:126.
-
(2010)
Genome Biol
, vol.11
, pp. 126
-
-
Marsh, J.A.1
Teichmann, S.A.2
-
45
-
-
84155175837
-
Quantifying the mechanisms of domain gain in animal proteins
-
Buljan M., Frankish A., Bateman A. Quantifying the mechanisms of domain gain in animal proteins. Genome Biol 2010, 11:R74.
-
(2010)
Genome Biol
, vol.11
, pp. R74
-
-
Buljan, M.1
Frankish, A.2
Bateman, A.3
-
46
-
-
84939207424
-
Most partial domains in proteins are alignment and annotation artifacts
-
Triant D.A., Pearson W.R. Most partial domains in proteins are alignment and annotation artifacts. Genome Biol 2015, 16:99.
-
(2015)
Genome Biol
, vol.16
, pp. 99
-
-
Triant, D.A.1
Pearson, W.R.2
-
47
-
-
84947269370
-
Emergence of de novo proteins from "dark genomic matter" by "grow slow and moult"
-
Bornberg-Bauer E., Schmitz J., Heberlein M. Emergence of de novo proteins from "dark genomic matter" by "grow slow and moult". Biochem Soc Trans 2015, 43:867-873.
-
(2015)
Biochem Soc Trans
, vol.43
, pp. 867-873
-
-
Bornberg-Bauer, E.1
Schmitz, J.2
Heberlein, M.3
-
48
-
-
84949979476
-
Detection of orphan domains in Drosophila using "hydrophobic cluster analysis"
-
Bitard-Feildel T., Heberlein M., Bornberg-Bauer E., Callebaut I. Detection of orphan domains in Drosophila using "hydrophobic cluster analysis". Biochimie 2015, 119:244-253.
-
(2015)
Biochimie
, vol.119
, pp. 244-253
-
-
Bitard-Feildel, T.1
Heberlein, M.2
Bornberg-Bauer, E.3
Callebaut, I.4
-
49
-
-
33646268799
-
Domain deletions and substitutions in the modular protein evolution
-
Weiner J., Beaussart F., Bornberg-Bauer E. Domain deletions and substitutions in the modular protein evolution. FEBS J 2006, 273:2037-2047.
-
(2006)
FEBS J
, vol.273
, pp. 2037-2047
-
-
Weiner, J.1
Beaussart, F.2
Bornberg-Bauer, E.3
-
50
-
-
70349319298
-
The evolution of protein domain families
-
Buljan M., Bateman A. The evolution of protein domain families. Biochem Soc Trans 2009, 37:751-755.
-
(2009)
Biochem Soc Trans
, vol.37
, pp. 751-755
-
-
Buljan, M.1
Bateman, A.2
-
51
-
-
84871827466
-
Genome-scale comparative analysis of gene fusions, gene fissions, and the fungal tree of life
-
Leonard G., Richards T.A. Genome-scale comparative analysis of gene fusions, gene fissions, and the fungal tree of life. Proc Natl Acad Sci U S A 2012, 109:21402-21407.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 21402-21407
-
-
Leonard, G.1
Richards, T.A.2
-
52
-
-
84939160343
-
Domain atrophy creates rare cases of functional partial protein domains
-
Prakash A., Bateman A. Domain atrophy creates rare cases of functional partial protein domains. Genome Biol 2015, 16:1-15.
-
(2015)
Genome Biol
, vol.16
, pp. 1-15
-
-
Prakash, A.1
Bateman, A.2
-
54
-
-
84879147679
-
The impact of splicing on protein domain architecture
-
Light S., Elofsson A., Gough J., Dunker A.K. The impact of splicing on protein domain architecture. Curr Opin Struct Biol 2013, 23:451-458.
-
(2013)
Curr Opin Struct Biol
, vol.23
, pp. 451-458
-
-
Light, S.1
Elofsson, A.2
Gough, J.3
Dunker, A.K.4
-
55
-
-
84958182784
-
Widespread expansion of protein interaction capabilities by alternative splicing
-
Yang X., Coulombe-Huntington J., Kang S., Sheynkman G.M., Hao T., Richardson A., Sun S., Yang F., Shen Y.A., Murray R.R., et al. Widespread expansion of protein interaction capabilities by alternative splicing. Cell 2016, 164:805-817.
-
(2016)
Cell
, vol.164
, pp. 805-817
-
-
Yang, X.1
Coulombe-Huntington, J.2
Kang, S.3
Sheynkman, G.M.4
Hao, T.5
Richardson, A.6
Sun, S.7
Yang, F.8
Shen, Y.A.9
Murray, R.R.10
-
56
-
-
84979866899
-
The evolutionary fate of alternatively spliced homologous exons after gene duplication
-
Abascal F., Tress M.L., Valencia A. The evolutionary fate of alternatively spliced homologous exons after gene duplication. Genome Biol 2015, 7:1392-1403.
-
(2015)
Genome Biol
, vol.7
, pp. 1392-1403
-
-
Abascal, F.1
Tress, M.L.2
Valencia, A.3
-
57
-
-
84942933058
-
Alternatively spliced homologous exons have ancient origins and are highly expressed at the protein level
-
Abascal F., Ezkurdia I., Rodriguez-Rivas J., Rodriguez J.M., del Pozo A., Vázquez J., Valencia A., Tress M.L. Alternatively spliced homologous exons have ancient origins and are highly expressed at the protein level. PLoS Comput Biol 2015, 11.
-
(2015)
PLoS Comput Biol
, vol.11
-
-
Abascal, F.1
Ezkurdia, I.2
Rodriguez-Rivas, J.3
Rodriguez, J.M.4
del Pozo, A.5
Vázquez, J.6
Valencia, A.7
Tress, M.L.8
-
58
-
-
84919700163
-
The modular structure of ThDP-dependent enzymes
-
Vogel C., Pleiss J. The modular structure of ThDP-dependent enzymes. Proteins 2014, 82:2523-2537.
-
(2014)
Proteins
, vol.82
, pp. 2523-2537
-
-
Vogel, C.1
Pleiss, J.2
-
59
-
-
84928253931
-
Panoramic view of a superfamily of phosphatases through substrate profiling
-
Huang H., Pandya C., Liu C., Al-Obaidi N.F., Wang M., Zheng L., Toews Keating S., Aono M., Love J.D., Evans B., et al. Panoramic view of a superfamily of phosphatases through substrate profiling. Proc Natl Acad Sci U S A 2015, 112:E1974-E1983.
-
(2015)
Proc Natl Acad Sci U S A
, vol.112
, pp. E1974-E1983
-
-
Huang, H.1
Pandya, C.2
Liu, C.3
Al-Obaidi, N.F.4
Wang, M.5
Zheng, L.6
Toews Keating, S.7
Aono, M.8
Love, J.D.9
Evans, B.10
-
60
-
-
84950324469
-
Promiscuity and electrostatic flexibility in the alkaline phosphatase superfamily
-
Pabis A., Kamerlin S.C.L. Promiscuity and electrostatic flexibility in the alkaline phosphatase superfamily. Curr Opin Struct Biol 2016, 37:14-21.
-
(2016)
Curr Opin Struct Biol
, vol.37
, pp. 14-21
-
-
Pabis, A.1
Kamerlin, S.C.L.2
-
61
-
-
84857510399
-
The role of robustness in phenotypic adaptation and innovation
-
Wagner A. The role of robustness in phenotypic adaptation and innovation. Proc R Soc B Biol Sci 2012, 279:1249-1258.
-
(2012)
Proc R Soc B Biol Sci
, vol.279
, pp. 1249-1258
-
-
Wagner, A.1
-
62
-
-
84934987986
-
Evolution of synthetic signaling scaffolds by recombination of modular protein domains
-
Lai A., Sato P.M., Peisajovich S.G. Evolution of synthetic signaling scaffolds by recombination of modular protein domains. ACS Synth Biol 2015, 4:714-722.
-
(2015)
ACS Synth Biol
, vol.4
, pp. 714-722
-
-
Lai, A.1
Sato, P.M.2
Peisajovich, S.G.3
-
63
-
-
85038121034
-
The robustness of a signaling complex to mutations that alter interaction specificities facilitates network evolution
-
Sato P.M., Yoganathan K., Jung J.H., Peisajovich S.G. The robustness of a signaling complex to mutations that alter interaction specificities facilitates network evolution. PLoS Biol 2012, 2012:e1002012.
-
(2012)
PLoS Biol
, vol.2012
, pp. e1002012
-
-
Sato, P.M.1
Yoganathan, K.2
Jung, J.H.3
Peisajovich, S.G.4
-
64
-
-
84924872598
-
Typical and atypical domain combinations in human protein kinases: functions, disease causing mutations and conservation in other primates
-
Rakshambikai R., Manoharan M., Gnanavel M., Srinivasan N. Typical and atypical domain combinations in human protein kinases: functions, disease causing mutations and conservation in other primates. RSC Adv 2015, 5:25132-25148.
-
(2015)
RSC Adv
, vol.5
, pp. 25132-25148
-
-
Rakshambikai, R.1
Manoharan, M.2
Gnanavel, M.3
Srinivasan, N.4
-
65
-
-
84961775708
-
Reading the combinatorial histone language
-
Su Z., Denu J.M. Reading the combinatorial histone language. ACS Chem Biol 2015, 10.1021/acschembio.5b00864.
-
(2015)
ACS Chem Biol
-
-
Su, Z.1
Denu, J.M.2
-
66
-
-
84946074739
-
The InterPro protein families database: the classification resource after 15 years
-
Mitchell A., Chang H.Y., Daugherty L., Fraser M., Hunter S., Lopez R., McAnulla C., McMenamin C., Nuka G., Pesseat S., et al. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res 2015, 43:D213-D221.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. D213-D221
-
-
Mitchell, A.1
Chang, H.Y.2
Daugherty, L.3
Fraser, M.4
Hunter, S.5
Lopez, R.6
McAnulla, C.7
McMenamin, C.8
Nuka, G.9
Pesseat, S.10
-
67
-
-
34548487255
-
Quantification of the elevated rate of domain rearrangements in metazoa
-
Ekman D., Björklund Å.K., Elofsson A. Quantification of the elevated rate of domain rearrangements in metazoa. J Mol Biol 2007, 372:1337-1348.
-
(2007)
J Mol Biol
, vol.372
, pp. 1337-1348
-
-
Ekman, D.1
Björklund Å, K.2
Elofsson, A.3
-
68
-
-
84928964293
-
Metazoans evolved by taking domains from soluble proteins to expand intercellular communication network
-
Nam H.-J., Kim I., Bowie J.U., Kim S. Metazoans evolved by taking domains from soluble proteins to expand intercellular communication network. Sci Rep 2015, 5:9576.
-
(2015)
Sci Rep
, vol.5
, pp. 9576
-
-
Nam, H.-J.1
Kim, I.2
Bowie, J.U.3
Kim, S.4
-
70
-
-
84964313946
-
Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes
-
Huang S., Chen Z., Yan X., Yu T., Huang G., Yan Q., Pontarotti P.A., Zhao H., Li J., Yang P., et al. Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes. Nat Commun 2014, 5:5896.
-
(2014)
Nat Commun
, vol.5
, pp. 5896
-
-
Huang, S.1
Chen, Z.2
Yan, X.3
Yu, T.4
Huang, G.5
Yan, Q.6
Pontarotti, P.A.7
Zhao, H.8
Li, J.9
Yang, P.10
-
71
-
-
84943568317
-
Function-selective domain architecture plasticity potentials in eukaryotic genome evolution
-
Linkeviciute V., Rackham O.J.L., Gough J., Oates M.E., Fang H. Function-selective domain architecture plasticity potentials in eukaryotic genome evolution. Biochimie 2015, 119:269-277.
-
(2015)
Biochimie
, vol.119
, pp. 269-277
-
-
Linkeviciute, V.1
Rackham, O.J.L.2
Gough, J.3
Oates, M.E.4
Fang, H.5
-
72
-
-
84937217426
-
New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM
-
Cromar G., Wong K.-C., Loughran N., On T., Song H., Xiong X., Zhang Z., Parkinson J. New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM. Genome Biol Evol 2014, 6:2897-2917.
-
(2014)
Genome Biol Evol
, vol.6
, pp. 2897-2917
-
-
Cromar, G.1
Wong, K.-C.2
Loughran, N.3
On, T.4
Song, H.5
Xiong, X.6
Zhang, Z.7
Parkinson, J.8
-
73
-
-
34047209861
-
Reactivation of mutant p53: molecular mechanisms and therapeutic potential
-
Selivanova G., Wiman K.G. Reactivation of mutant p53: molecular mechanisms and therapeutic potential. Oncogene 2007, 26:2243-2254.
-
(2007)
Oncogene
, vol.26
, pp. 2243-2254
-
-
Selivanova, G.1
Wiman, K.G.2
-
74
-
-
84926389300
-
Protein domain-level landscape of cancer-type-specific somatic mutations
-
Yang F., Petsalaki E., Rolland T., Hill D.E., Vidal M., Roth F.P. Protein domain-level landscape of cancer-type-specific somatic mutations. PLoS Comput Biol 2015, 11.
-
(2015)
PLoS Comput Biol
, vol.11
-
-
Yang, F.1
Petsalaki, E.2
Rolland, T.3
Hill, D.E.4
Vidal, M.5
Roth, F.P.6
-
75
-
-
84930939029
-
Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains
-
Shi J., Wang E., Milazzo J.P., Wang Z., Kinney J.B., Vakoc C.R. Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nat Biotechnol 2015, 33:1-10.
-
(2015)
Nat Biotechnol
, vol.33
, pp. 1-10
-
-
Shi, J.1
Wang, E.2
Milazzo, J.P.3
Wang, Z.4
Kinney, J.B.5
Vakoc, C.R.6
-
76
-
-
84988603266
-
Integrated sequence and expression analysis of ovarian cancer structural variants underscores the importance of gene fusion regulation
-
Mittal V.K., McDonald J.F. Integrated sequence and expression analysis of ovarian cancer structural variants underscores the importance of gene fusion regulation. BMC Med Genomics 2015, 8:40.
-
(2015)
BMC Med Genomics
, vol.8
, pp. 40
-
-
Mittal, V.K.1
McDonald, J.F.2
-
77
-
-
84865805666
-
Transforming fusions of FGFR and TACC genes in human glioblastoma
-
Singh D., Chan J.M., Zoppoli P., Niola F., Sullivan R., Castano A., Liu E.M., Reichel J., Porrati P., Pellegatta S., et al. Transforming fusions of FGFR and TACC genes in human glioblastoma. Science 2012, 337:1231-1235.
-
(2012)
Science
, vol.337
, pp. 1231-1235
-
-
Singh, D.1
Chan, J.M.2
Zoppoli, P.3
Niola, F.4
Sullivan, R.5
Castano, A.6
Liu, E.M.7
Reichel, J.8
Porrati, P.9
Pellegatta, S.10
-
78
-
-
84922373207
-
The landscape of kinase fusions in cancer
-
Stransky N., Cerami E., Schalm S., Kim J.L., Lengauer C. The landscape of kinase fusions in cancer. Nat Commun 2014, 5:4846.
-
(2014)
Nat Commun
, vol.5
, pp. 4846
-
-
Stransky, N.1
Cerami, E.2
Schalm, S.3
Kim, J.L.4
Lengauer, C.5
-
79
-
-
65449183174
-
Signatures of selection in fusion transcripts resulting from chromosomal translocations in human cancer
-
Ortiz de Mendíbil I., Vizmanos J.L., Novo F.J. Signatures of selection in fusion transcripts resulting from chromosomal translocations in human cancer. PLoS ONE 2009, 4.
-
(2009)
PLoS ONE
, vol.4
-
-
Ortiz de Mendíbil, I.1
Vizmanos, J.L.2
Novo, F.J.3
-
80
-
-
84885588233
-
Oncofuse: a computational framework for the prediction of the oncogenic potential of gene fusions
-
Shugay M., De Mendíbil I.O., Vizmanos J.L., Novo F.J. Oncofuse: a computational framework for the prediction of the oncogenic potential of gene fusions. Bioinformatics 2013, 29:2539-2546.
-
(2013)
Bioinformatics
, vol.29
, pp. 2539-2546
-
-
Shugay, M.1
De Mendíbil, I.O.2
Vizmanos, J.L.3
Novo, F.J.4
-
81
-
-
84863512195
-
Novel domain combinations in proteins encoded by chimeric transcripts
-
Frenkel-Morgenstern M., Valencia A. Novel domain combinations in proteins encoded by chimeric transcripts. Bioinformatics 2012, 28:i67-i74.
-
(2012)
Bioinformatics
, vol.28
, pp. i67-i74
-
-
Frenkel-Morgenstern, M.1
Valencia, A.2
-
82
-
-
75549086174
-
Eukaryotic protein domains as functional units of cellular evolution
-
ra76
-
Jin J., Xie X., Chen C., Park J.G., Stark C., James D.A., Olhovsky M., Linding R., Mao Y., Pawson T. Eukaryotic protein domains as functional units of cellular evolution. Sci Signal 2009, 2:ra76.
-
(2009)
Sci Signal
, vol.2
-
-
Jin, J.1
Xie, X.2
Chen, C.3
Park, J.G.4
Stark, C.5
James, D.A.6
Olhovsky, M.7
Linding, R.8
Mao, Y.9
Pawson, T.10
-
83
-
-
84884618426
-
Rewiring cell signalling through chimaeric regulatory protein engineering
-
Wang B., Barahona M., Buck M., Schumacher J. Rewiring cell signalling through chimaeric regulatory protein engineering. Biochem Soc Trans 2013, 41:1195-1200.
-
(2013)
Biochem Soc Trans
, vol.41
, pp. 1195-1200
-
-
Wang, B.1
Barahona, M.2
Buck, M.3
Schumacher, J.4
-
84
-
-
77952944052
-
Designing customized cell signalling circuits
-
Lim W.A. Designing customized cell signalling circuits. Nat Rev Mol Cell Biol 2010, 11:393-403.
-
(2010)
Nat Rev Mol Cell Biol
, vol.11
, pp. 393-403
-
-
Lim, W.A.1
|