-
1
-
-
84861511557
-
The emergence of protein complexes: quaternary structure, dynamics and allostery
-
Perica T., Marsh J.A., Sousa F.L., Natan E., Colwell L.J., Ahnert S.E., Teichmann S.A. The emergence of protein complexes: quaternary structure, dynamics and allostery. Biochem Soc Trans 2012, 40:475-491.
-
(2012)
Biochem Soc Trans
, vol.40
, pp. 475-491
-
-
Perica, T.1
Marsh, J.A.2
Sousa, F.L.3
Natan, E.4
Colwell, L.J.5
Ahnert, S.E.6
Teichmann, S.A.7
-
2
-
-
0041312697
-
Diversity of protein-protein interactions
-
Nooren I.M.A., Thornton J.M. Diversity of protein-protein interactions. EMBO J 2003, 22:3486-3492.
-
(2003)
EMBO J
, vol.22
, pp. 3486-3492
-
-
Nooren, I.M.A.1
Thornton, J.M.2
-
3
-
-
77957921373
-
A simple definition of structural regions in proteins and its use in analyzing interface evolution
-
Levy E.D. A simple definition of structural regions in proteins and its use in analyzing interface evolution. J Mol Biol 2010, 403:660-670.
-
(2010)
J Mol Biol
, vol.403
, pp. 660-670
-
-
Levy, E.D.1
-
4
-
-
0003187567
-
The atomic structure of protein-protein recognition sites
-
Lo Conte L., Chothia C., Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol 1999, 285:2177-2198.
-
(1999)
J Mol Biol
, vol.285
, pp. 2177-2198
-
-
Lo Conte, L.1
Chothia, C.2
Janin, J.3
-
5
-
-
77949609215
-
Atomic interaction networks in the core of protein domains and their native folds
-
Soundararajan V., Raman R., Raguram S., Sasisekharan V., Sasisekharan R. Atomic interaction networks in the core of protein domains and their native folds. PLoS ONE 2010, 5:e9391.
-
(2010)
PLoS ONE
, vol.5
-
-
Soundararajan, V.1
Raman, R.2
Raguram, S.3
Sasisekharan, V.4
Sasisekharan, R.5
-
6
-
-
84873685831
-
Molecular signatures of G-protein-coupled receptors
-
Venkatakrishnan A.J., Deupi X., Lebon G., Tate C.G., Schertler G.F., Babu M.M. Molecular signatures of G-protein-coupled receptors. Nature 2013, 494:185-194.
-
(2013)
Nature
, vol.494
, pp. 185-194
-
-
Venkatakrishnan, A.J.1
Deupi, X.2
Lebon, G.3
Tate, C.G.4
Schertler, G.F.5
Babu, M.M.6
-
7
-
-
52649130704
-
Protein-protein interaction and quaternary structure
-
Janin J., Bahadur R.P., Chakrabarti P. Protein-protein interaction and quaternary structure. Q Rev Biophys 2008, 41:133-180.
-
(2008)
Q Rev Biophys
, vol.41
, pp. 133-180
-
-
Janin, J.1
Bahadur, R.P.2
Chakrabarti, P.3
-
8
-
-
84875901122
-
Intertwined associations in structures of homooligomeric proteins
-
Mackinnon S.S., Malevanets A., Wodak S.J. Intertwined associations in structures of homooligomeric proteins. Structure 2013, 21:638-649.
-
(2013)
Structure
, vol.21
, pp. 638-649
-
-
Mackinnon, S.S.1
Malevanets, A.2
Wodak, S.J.3
-
9
-
-
84879549646
-
What makes a protein fold amenable to functional innovation? Fold polarity and stability trade-offs
-
[Internet]
-
Dellus-Gur E., Tóth-Petróczy 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, [Internet]. 10.1016/j.jmb.2013.03.033.
-
(2013)
J Mol Biol
-
-
Dellus-Gur, E.1
Tóth-Petróczy, A.2
Elias, M.3
Tawfik, D.S.4
-
10
-
-
80052326913
-
Transient protein-protein interactions
-
Ozbabacan S.E.A., Engin H.B., Gursoy A., Keskin O. Transient protein-protein interactions. Protein Eng Des Sel 2011, 24:635-648.
-
(2011)
Protein Eng Des Sel
, vol.24
, pp. 635-648
-
-
Ozbabacan, S.E.A.1
Engin, H.B.2
Gursoy, A.3
Keskin, O.4
-
11
-
-
70349229596
-
Dynamic interactions of proteins in complex networks: a more structured view
-
Stein A., Pache R.A., Bernadó P., Pons M., Aloy P. Dynamic interactions of proteins in complex networks: a more structured view. FEBS J 2009, 276:5390-5405.
-
(2009)
FEBS J
, vol.276
, pp. 5390-5405
-
-
Stein, A.1
Pache, R.A.2
Bernadó, P.3
Pons, M.4
Aloy, P.5
-
12
-
-
84861119844
-
Network evolution: rewiring and signatures of conservation in signaling
-
Sun M.G.F., Sikora M., Costanzo M., Boone C., Kim P.M. Network evolution: rewiring and signatures of conservation in signaling. PLoS Comput Biol 2012, 8:e1002411.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Sun, M.G.F.1
Sikora, M.2
Costanzo, M.3
Boone, C.4
Kim, P.M.5
-
13
-
-
20444414545
-
Linear motifs: evolutionary interaction switches
-
Neduva V., Russell R.B. Linear motifs: evolutionary interaction switches. FEBS Lett 2005, 579:3342-3345.
-
(2005)
FEBS Lett
, vol.579
, pp. 3342-3345
-
-
Neduva, V.1
Russell, R.B.2
-
14
-
-
77957771797
-
Transient protein-protein interactions: structural, functional, and network properties
-
Perkins J.R., Diboun I., Dessailly B.H., Lees J.G., Orengo C. Transient protein-protein interactions: structural, functional, and network properties. Structure 2010, 18:1233-1243.
-
(2010)
Structure
, vol.18
, pp. 1233-1243
-
-
Perkins, J.R.1
Diboun, I.2
Dessailly, B.H.3
Lees, J.G.4
Orengo, C.5
-
15
-
-
0028916599
-
A hot spot of binding energy in a hormone-receptor interface
-
Clackson T., Wells J.A. A hot spot of binding energy in a hormone-receptor interface. Science 1995, 267:383-386.
-
(1995)
Science
, vol.267
, pp. 383-386
-
-
Clackson, T.1
Wells, J.A.2
-
16
-
-
84872225092
-
On the binding affinity of macromolecular interactions: daring to ask why proteins interact
-
Kastritis P.L., Bonvin A.M.J.J. On the binding affinity of macromolecular interactions: daring to ask why proteins interact. J R Soc Interface 2013, 10:20120835.
-
(2013)
J R Soc Interface
, vol.10
, pp. 20120835
-
-
Kastritis, P.L.1
Bonvin, A.M.J.J.2
-
17
-
-
34548779127
-
Hot spots-a review of the protein-protein interface determinant amino-acid residues
-
Moreira I.S., Fernandes P.A., Ramos M.J. Hot spots-a review of the protein-protein interface determinant amino-acid residues. Proteins 2007, 68:803-812.
-
(2007)
Proteins
, vol.68
, pp. 803-812
-
-
Moreira, I.S.1
Fernandes, P.A.2
Ramos, M.J.3
-
18
-
-
0032479179
-
Anatomy of hot spots in protein interfaces
-
Bogan A., Thorn K. Anatomy of hot spots in protein interfaces. J Mol Biol 1998, 280:1-9.
-
(1998)
J Mol Biol
, vol.280
, pp. 1-9
-
-
Bogan, A.1
Thorn, K.2
-
19
-
-
0034213559
-
Conservation of polar residues as hot spots at protein interfaces
-
Hu Z., Ma B., Wolfson H., Nussinov R. Conservation of polar residues as hot spots at protein interfaces. Proteins 2000, 39:331-342.
-
(2000)
Proteins
, vol.39
, pp. 331-342
-
-
Hu, Z.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
20
-
-
0037093645
-
Dissecting protein-protein recognition sites
-
Chakrabarti P., Janin J. Dissecting protein-protein recognition sites. Proteins 2002, 47:334-343.
-
(2002)
Proteins
, vol.47
, pp. 334-343
-
-
Chakrabarti, P.1
Janin, J.2
-
21
-
-
0346733329
-
Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
-
Caffrey D.R., Somaroo S., Hughes J.D., Mintseris J., Huang E.S. Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?. Protein Sci 2004, 13:190-202.
-
(2004)
Protein Sci
, vol.13
, pp. 190-202
-
-
Caffrey, D.R.1
Somaroo, S.2
Hughes, J.D.3
Mintseris, J.4
Huang, E.S.5
-
22
-
-
27344440132
-
Conservation and relative importance of residues across protein-protein interfaces
-
Guharoy M., Chakrabarti P. Conservation and relative importance of residues across protein-protein interfaces. Proc Natl Acad Sci U S A 2005, 102:15447-15452.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 15447-15452
-
-
Guharoy, M.1
Chakrabarti, P.2
-
23
-
-
23344451687
-
Structure, function, and evolution of transient and obligate protein-protein interactions
-
Mintseris J., Weng Z. Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci U S A 2005, 102:10930-10935.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 10930-10935
-
-
Mintseris, J.1
Weng, Z.2
-
24
-
-
79954633234
-
A de novo protein binding pair by computational design and directed evolution
-
Karanicolas J., Corn J.E., Chen I., Joachimiak L.A., Dym O., Peck S.H., Albeck S., Unger T., Hu W., Liu G., et al. A de novo protein binding pair by computational design and directed evolution. Mol Cell 2011, 42:250-260.
-
(2011)
Mol Cell
, vol.42
, pp. 250-260
-
-
Karanicolas, J.1
Corn, J.E.2
Chen, I.3
Joachimiak, L.A.4
Dym, O.5
Peck, S.H.6
Albeck, S.7
Unger, T.8
Hu, W.9
Liu, G.10
-
25
-
-
51649094321
-
Built-in loops allow versatility in domain-domain interactions: lessons from self-interacting domains
-
Akiva E., Itzhaki Z., Margalit H. Built-in loops allow versatility in domain-domain interactions: lessons from self-interacting domains. Proc Natl Acad Sci U S A 2008, 105:13292-13297.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 13292-13297
-
-
Akiva, E.1
Itzhaki, Z.2
Margalit, H.3
-
26
-
-
78650537920
-
Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states
-
Hashimoto K., Panchenko A.R. Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states. Proc Natl Acad Sci U S A 2010, 107:20352-20357.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 20352-20357
-
-
Hashimoto, K.1
Panchenko, A.R.2
-
27
-
-
79960090510
-
Cover and spacer insertions: small nonhydrophobic accessories that assist protein oligomerization
-
Nishi H., Koike R., Ota M. Cover and spacer insertions: small nonhydrophobic accessories that assist protein oligomerization. Proteins 2011, 79:2372-2379.
-
(2011)
Proteins
, vol.79
, pp. 2372-2379
-
-
Nishi, H.1
Koike, R.2
Ota, M.3
-
28
-
-
84859467082
-
Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair
-
Kapp G.T., Liu S., Stein A., Wong D.T., Reményi A., Yeh B.J., Fraser J.S., Taunton J., Lim W.A., Kortemme T. Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair. Proc Natl Acad Sci U S A 2012, 109:5277-5282.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 5277-5282
-
-
Kapp, G.T.1
Liu, S.2
Stein, A.3
Wong, D.T.4
Reményi, A.5
Yeh, B.J.6
Fraser, J.S.7
Taunton, J.8
Lim, W.A.9
Kortemme, T.10
-
29
-
-
70350033973
-
Dissecting an allosteric switch in caspase-7 using chemical and mutational probes
-
Hardy J.A., Wells J.A. Dissecting an allosteric switch in caspase-7 using chemical and mutational probes. J Biol Chem 2009, 284:26063-26069.
-
(2009)
J Biol Chem
, vol.284
, pp. 26063-26069
-
-
Hardy, J.A.1
Wells, J.A.2
-
30
-
-
84861450634
-
Evolution of oligomeric state through geometric coupling of protein interfaces
-
Perica T., Chothia C., Teichmann S.A. Evolution of oligomeric state through geometric coupling of protein interfaces. Proc Natl Acad Sci U S A 2012, 109:8127-8132.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 8127-8132
-
-
Perica, T.1
Chothia, C.2
Teichmann, S.A.3
-
31
-
-
0029587166
-
A method to predict functional residues in proteins
-
Casari G., Sander C., Valencia A. A method to predict functional residues in proteins. Nat Struct Biol 1995, 2:171-178.
-
(1995)
Nat Struct Biol
, vol.2
, pp. 171-178
-
-
Casari, G.1
Sander, C.2
Valencia, A.3
-
32
-
-
84875225476
-
Emerging methods in protein co-evolution
-
De Juan D., Pazos F., Valencia A. Emerging methods in protein co-evolution. Nat Rev Genet 2013, 14:249-261.
-
(2013)
Nat Rev Genet
, vol.14
, pp. 249-261
-
-
De Juan, D.1
Pazos, F.2
Valencia, A.3
-
33
-
-
44649153450
-
Rewiring the specificity of two-component signal transduction systems
-
Skerker J.M., Perchuk B.S., Siryaporn A., Lubin E.A., Ashenberg O., Goulian M., Laub M.T. Rewiring the specificity of two-component signal transduction systems. Cell 2008, 133:1043-1054.
-
(2008)
Cell
, vol.133
, pp. 1043-1054
-
-
Skerker, J.M.1
Perchuk, B.S.2
Siryaporn, A.3
Lubin, E.A.4
Ashenberg, O.5
Goulian, M.6
Laub, M.T.7
-
34
-
-
68749107059
-
Protein sectors: evolutionary units of three-dimensional structure
-
Halabi N., Rivoire O., Leibler S., Ranganathan R. Protein sectors: evolutionary units of three-dimensional structure. Cell 2009, 138:774-786.
-
(2009)
Cell
, vol.138
, pp. 774-786
-
-
Halabi, N.1
Rivoire, O.2
Leibler, S.3
Ranganathan, R.4
-
35
-
-
0345374584
-
The structure of importin-beta bound to SREBP-2: nuclear import of a transcription factor
-
Lee S.J., Sekimoto T., Yamashita E., Nagoshi E., Nakagawa A., Imamoto N., Yoshimura M., Sakai H., Chong K.T., Tsukihara T., et al. The structure of importin-beta bound to SREBP-2: nuclear import of a transcription factor. Science 2003, 302:1571-1575.
-
(2003)
Science
, vol.302
, pp. 1571-1575
-
-
Lee, S.J.1
Sekimoto, T.2
Yamashita, E.3
Nagoshi, E.4
Nakagawa, A.5
Imamoto, N.6
Yoshimura, M.7
Sakai, H.8
Chong, K.T.9
Tsukihara, T.10
-
36
-
-
1342302339
-
Conformational changes associated with protein-protein interactions
-
Goh C.-S., Milburn D., Gerstein M. Conformational changes associated with protein-protein interactions. Curr Opin Struct Biol 2004, 14:104-109.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 104-109
-
-
Goh, C.-S.1
Milburn, D.2
Gerstein, M.3
-
37
-
-
0034595516
-
Co-evolution of proteins with their interaction partners
-
Goh C.S., Bogan A.A., Joachimiak M., Walther D., Cohen F.E. Co-evolution of proteins with their interaction partners. J Mol Biol 2000, 299:283-293.
-
(2000)
J Mol Biol
, vol.299
, pp. 283-293
-
-
Goh, C.S.1
Bogan, A.A.2
Joachimiak, M.3
Walther, D.4
Cohen, F.E.5
-
38
-
-
0035177259
-
Similarity of phylogenetic trees as indicator of protein-protein interaction
-
Pazos F., Valencia A. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng 2001, 14:609-614.
-
(2001)
Protein Eng
, vol.14
, pp. 609-614
-
-
Pazos, F.1
Valencia, A.2
-
39
-
-
84862647180
-
Three-dimensional structures of membrane proteins from genomic sequencing
-
Hopf T.A., Colwell L.J., Sheridan R., Rost B., Sander C., Marks D.S. Three-dimensional structures of membrane proteins from genomic sequencing. Cell 2012, 149:1607-1621.
-
(2012)
Cell
, vol.149
, pp. 1607-1621
-
-
Hopf, T.A.1
Colwell, L.J.2
Sheridan, R.3
Rost, B.4
Sander, C.5
Marks, D.S.6
-
40
-
-
28444463255
-
Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis
-
Choi S.S., Li W., Lahn B.T. Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis. Nat Genet 2005, 37:1367-1371.
-
(2005)
Nat Genet
, vol.37
, pp. 1367-1371
-
-
Choi, S.S.1
Li, W.2
Lahn, B.T.3
-
41
-
-
58549114185
-
Identification of direct residue contacts in protein-protein interaction by message passing
-
Weigt M., White R.A., Szurmant H., Hoch J.A., Hwa T. Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci U S A 2009, 106:67-72.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 67-72
-
-
Weigt, M.1
White, R.A.2
Szurmant, H.3
Hoch, J.A.4
Hwa, T.5
-
42
-
-
84455167671
-
Hot spots for allosteric regulation on protein surfaces
-
Reynolds K.A., McLaughlin R.N., Ranganathan R. Hot spots for allosteric regulation on protein surfaces. Cell 2011, 147:1564-1575.
-
(2011)
Cell
, vol.147
, pp. 1564-1575
-
-
Reynolds, K.A.1
McLaughlin, R.N.2
Ranganathan, R.3
-
43
-
-
0013863816
-
Comparison of experimental binding data and theoretical models in proteins containing subunits
-
Koshland D.E., Némethy G., Filmer D. Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 1966, 5:365-385.
-
(1966)
Biochemistry
, vol.5
, pp. 365-385
-
-
Koshland, D.E.1
Némethy, G.2
Filmer, D.3
-
44
-
-
0021658956
-
Allostery without conformational change. A plausible model
-
Cooper A., Dryden D.T. Allostery without conformational change. A plausible model. Eur Biophys J 1984, 11:103-109.
-
(1984)
Eur Biophys J
, vol.11
, pp. 103-109
-
-
Cooper, A.1
Dryden, D.T.2
-
45
-
-
73449144096
-
Dynamic allostery in the methionine repressor revealed by force distribution analysis
-
Stacklies W., Xia F., Gräter F. Dynamic allostery in the methionine repressor revealed by force distribution analysis. PLoS Comput Biol 2009, 5:e1000574.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Stacklies, W.1
Xia, F.2
Gräter, F.3
-
46
-
-
78149473070
-
Allostery and population shift in drug discovery
-
Kar G., Keskin O., Gursoy A., Nussinov R. Allostery and population shift in drug discovery. Curr Opin Pharmacol 2010, 10:715-722.
-
(2010)
Curr Opin Pharmacol
, vol.10
, pp. 715-722
-
-
Kar, G.1
Keskin, O.2
Gursoy, A.3
Nussinov, R.4
-
47
-
-
68149157248
-
The origin of allosteric functional modulation: multiple pre-existing pathways
-
Del Sol A., Tsai C.-J., Ma B., Nussinov R. The origin of allosteric functional modulation: multiple pre-existing pathways. Structure 2009, 17:1042-1050.
-
(2009)
Structure
, vol.17
, pp. 1042-1050
-
-
Del Sol, A.1
Tsai, C.-J.2
Ma, B.3
Nussinov, R.4
-
48
-
-
41149104308
-
Allostery: absence of a change in shape does not imply that allostery is not at play
-
Tsai C.-J., del Sol A., Nussinov R. Allostery: absence of a change in shape does not imply that allostery is not at play. J Mol Biol 2008, 378:1-11.
-
(2008)
J Mol Biol
, vol.378
, pp. 1-11
-
-
Tsai, C.-J.1
del Sol, A.2
Nussinov, R.3
-
49
-
-
0037219686
-
Evolutionarily conserved networks of residues mediate allosteric communication in proteins
-
Süel G.M., Lockless S.W., Wall M.A., Ranganathan R. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol 2003, 10:59-69.
-
(2003)
Nat Struct Biol
, vol.10
, pp. 59-69
-
-
Süel, G.M.1
Lockless, S.W.2
Wall, M.A.3
Ranganathan, R.4
-
50
-
-
74549149999
-
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure
-
Capra J.A., Laskowski R.A., Thornton J.M., Singh M., Funkhouser T.A. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput Biol 2009, 5:e1000585.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Capra, J.A.1
Laskowski, R.A.2
Thornton, J.M.3
Singh, M.4
Funkhouser, T.A.5
-
51
-
-
75849116590
-
A minimal sequence code for switching protein structure and function
-
Alexander P.A., He Y., Chen Y., Orban J., Bryan P.N. A minimal sequence code for switching protein structure and function. Proc Natl Acad Sci U S A 2009, 106:21149-21154.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 21149-21154
-
-
Alexander, P.A.1
He, Y.2
Chen, Y.3
Orban, J.4
Bryan, P.N.5
-
52
-
-
84863012003
-
Mutational tipping points for switching protein folds and functions
-
He Y., Chen Y., Alexander P.A., Bryan P.N., Orban J. Mutational tipping points for switching protein folds and functions. Structure 2012, 20:283-291.
-
(2012)
Structure
, vol.20
, pp. 283-291
-
-
He, Y.1
Chen, Y.2
Alexander, P.A.3
Bryan, P.N.4
Orban, J.5
-
53
-
-
84865306330
-
Directed enzyme evolution: beyond the low-hanging fruit
-
Goldsmith M., Tawfik D.S. Directed enzyme evolution: beyond the low-hanging fruit. Curr Opin Struct Biol 2012, 22:406-412.
-
(2012)
Curr Opin Struct Biol
, vol.22
, pp. 406-412
-
-
Goldsmith, M.1
Tawfik, D.S.2
-
54
-
-
34547499110
-
The design and characterization of two proteins with 88% sequence identity but different structure and function
-
Alexander P.A., He Y., Chen Y., Orban J., Bryan P.N. The design and characterization of two proteins with 88% sequence identity but different structure and function. Proc Natl Acad Sci U S A 2007, 104:11963-11968.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 11963-11968
-
-
Alexander, P.A.1
He, Y.2
Chen, Y.3
Orban, J.4
Bryan, P.N.5
-
55
-
-
0036139093
-
Why are proteins marginally stable?
-
Taverna D.M., Goldstein R.A. Why are proteins marginally stable?. Proteins 2002, 46:105-109.
-
(2002)
Proteins
, vol.46
, pp. 105-109
-
-
Taverna, D.M.1
Goldstein, R.A.2
-
56
-
-
70349901079
-
Stability effects of mutations and protein evolvability
-
Tokuriki N., Tawfik D.S. Stability effects of mutations and protein evolvability. Curr Opin Struct Biol 2009, 19:596-604.
-
(2009)
Curr Opin Struct Biol
, vol.19
, pp. 596-604
-
-
Tokuriki, N.1
Tawfik, D.S.2
-
57
-
-
33645811495
-
Protein stability promotes evolvability
-
Bloom J.D., Labthavikul S.T., Otey C.R., Arnold F.H. Protein stability promotes evolvability. Proc Natl Acad Sci U S A 2006, 103:5869-5874.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 5869-5874
-
-
Bloom, J.D.1
Labthavikul, S.T.2
Otey, C.R.3
Arnold, F.H.4
-
58
-
-
0036306115
-
Why are proteins so robust to site mutations?
-
Taverna D.M., Goldstein R.A. Why are proteins so robust to site mutations?. J Mol Biol 2002, 315:479-484.
-
(2002)
J Mol Biol
, vol.315
, pp. 479-484
-
-
Taverna, D.M.1
Goldstein, R.A.2
-
59
-
-
33645790071
-
Simple and accurate estimation of ancestral protein sequences
-
Hall B.G. Simple and accurate estimation of ancestral protein sequences. Proc Natl Acad Sci U S A 2006, 103:5431-5436.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 5431-5436
-
-
Hall, B.G.1
-
61
-
-
34548040966
-
Crystal structure of an ancient protein: evolution by conformational epistasis
-
Ortlund E.A., Bridgham J.T., Redinbo M.R., Thornton J.W. Crystal structure of an ancient protein: evolution by conformational epistasis. Science 2007, 317:1544-1548.
-
(2007)
Science
, vol.317
, pp. 1544-1548
-
-
Ortlund, E.A.1
Bridgham, J.T.2
Redinbo, M.R.3
Thornton, J.W.4
-
62
-
-
70349464621
-
An epistatic ratchet constrains the direction of glucocorticoid receptor evolution
-
Bridgham J.T., Ortlund E.A., Thornton J.W. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 2009, 461:515-519.
-
(2009)
Nature
, vol.461
, pp. 515-519
-
-
Bridgham, J.T.1
Ortlund, E.A.2
Thornton, J.W.3
-
63
-
-
84855870416
-
On the origin and evolution of thermophily: reconstruction of functional precambrian enzymes from ancestors of bacillus
-
Hobbs J.K., Shepherd C., Saul D.J., Demetras N.J., Haaning S., Monk C.R., Daniel R.M., Arcus V.L. On the origin and evolution of thermophily: reconstruction of functional precambrian enzymes from ancestors of bacillus. Mol Biol Evol 2012, 29:825-835.
-
(2012)
Mol Biol Evol
, vol.29
, pp. 825-835
-
-
Hobbs, J.K.1
Shepherd, C.2
Saul, D.J.3
Demetras, N.J.4
Haaning, S.5
Monk, C.R.6
Daniel, R.M.7
Arcus, V.L.8
-
64
-
-
84879064073
-
Stability-mediated epistasis constrains the evolution of an influenza protein
-
Gong L.I., Suchard M.A., Bloom J.D. Stability-mediated epistasis constrains the evolution of an influenza protein. Elife 2013, 2:e00631.
-
(2013)
Elife
, vol.2
-
-
Gong, L.I.1
Suchard, M.A.2
Bloom, J.D.3
-
65
-
-
84865075179
-
A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function
-
[Internet]
-
Lai J., Jin J., Kubelka J., Liberles D.A. A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function. J Mol Biol 2012, [Internet]. 10.1016/j.jmb.2012.05.028.
-
(2012)
J Mol Biol
-
-
Lai, J.1
Jin, J.2
Kubelka, J.3
Liberles, D.A.4
-
66
-
-
34547153905
-
The selection of acceptable protein mutations
-
Sasidharan R., Chothia C. The selection of acceptable protein mutations. Proc Natl Acad Sci U S A 2007, 104:10080-10085.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 10080-10085
-
-
Sasidharan, R.1
Chothia, C.2
-
67
-
-
79960601166
-
Slow protein evolutionary rates are dictated by surface-core association
-
Tóth-Petróczy A., Tawfik D.S. Slow protein evolutionary rates are dictated by surface-core association. Proc Natl Acad Sci U S A 2011, 108:11151-11156.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 11151-11156
-
-
Tóth-Petróczy, A.1
Tawfik, D.S.2
-
68
-
-
84870901239
-
Cellular crowding imposes global constraints on the chemistry and evolution of proteomes
-
Levy E.D., De S., Teichmann S.A. Cellular crowding imposes global constraints on the chemistry and evolution of proteomes. Proc Natl Acad Sci U S A 2012, 109:20461-20466.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 20461-20466
-
-
Levy, E.D.1
De, S.2
Teichmann, S.A.3
-
69
-
-
70349318376
-
Structure is three to ten times more conserved than sequence-a study of structural response in protein cores
-
Illergård K., Ardell D.H., Elofsson A. Structure is three to ten times more conserved than sequence-a study of structural response in protein cores. Proteins 2009, 77:499-508.
-
(2009)
Proteins
, vol.77
, pp. 499-508
-
-
Illergård, K.1
Ardell, D.H.2
Elofsson, A.3
-
70
-
-
0036892389
-
Thoroughly sampling sequence space: large-scale protein design of structural ensembles
-
Larson S.M., England J.L., Desjarlais J.R., Pande V.S. Thoroughly sampling sequence space: large-scale protein design of structural ensembles. Protein Sci 2002, 11:2804-2813.
-
(2002)
Protein Sci
, vol.11
, pp. 2804-2813
-
-
Larson, S.M.1
England, J.L.2
Desjarlais, J.R.3
Pande, V.S.4
-
71
-
-
15544390249
-
Protein structure and evolutionary history determine sequence space topology
-
Shakhnovich B.E., Deeds E., Delisi C., Shakhnovich E. Protein structure and evolutionary history determine sequence space topology. Genome Res 2005, 15:385-392.
-
(2005)
Genome Res
, vol.15
, pp. 385-392
-
-
Shakhnovich, B.E.1
Deeds, E.2
Delisi, C.3
Shakhnovich, E.4
-
72
-
-
84871839239
-
Protein conformational diversity modulates sequence divergence
-
Juritz E., Palopoli N., Fornasari M.S., Fernandez-Alberti S., Parisi G. Protein conformational diversity modulates sequence divergence. Mol Biol Evol 2013, 30:79-87.
-
(2013)
Mol Biol Evol
, vol.30
, pp. 79-87
-
-
Juritz, E.1
Palopoli, N.2
Fornasari, M.S.3
Fernandez-Alberti, S.4
Parisi, G.5
-
73
-
-
77955579347
-
Designing ensembles in conformational and sequence space to characterize and engineer proteins
-
Friedland G.D., Kortemme T. Designing ensembles in conformational and sequence space to characterize and engineer proteins. Curr Opin Struct Biol 2010, 20:377-384.
-
(2010)
Curr Opin Struct Biol
, vol.20
, pp. 377-384
-
-
Friedland, G.D.1
Kortemme, T.2
-
74
-
-
67049155677
-
A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family
-
Friedland G.D., Lakomek N.-A., Griesinger C., Meiler J., Kortemme T. A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput Biol 2009, 5:e1000393.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Friedland, G.D.1
Lakomek, N.-A.2
Griesinger, C.3
Meiler, J.4
Kortemme, T.5
-
75
-
-
43549093267
-
Evolutionary divergence of protein structure: the linearly forced elastic network model
-
Echave J. Evolutionary divergence of protein structure: the linearly forced elastic network model. Chem Phys Lett 2008, 457:413-416.
-
(2008)
Chem Phys Lett
, vol.457
, pp. 413-416
-
-
Echave, J.1
-
76
-
-
8544221118
-
Network analysis of protein structures identifies functional residues
-
Amitai G., Shemesh A., Sitbon E., Shklar M., Netanely D., Venger I., Pietrokovski S. Network analysis of protein structures identifies functional residues. J Mol Biol 2004, 344:1135-1146.
-
(2004)
J Mol Biol
, vol.344
, pp. 1135-1146
-
-
Amitai, G.1
Shemesh, A.2
Sitbon, E.3
Shklar, M.4
Netanely, D.5
Venger, I.6
Pietrokovski, S.7
-
77
-
-
41949141017
-
Proteins as networks: usefulness of graph theory in protein science
-
Krishnan A., Zbilut J.P., Tomita M., Giuliani A. Proteins as networks: usefulness of graph theory in protein science. Curr Protein Pept Sci 2008, 9:28-38.
-
(2008)
Curr Protein Pept Sci
, vol.9
, pp. 28-38
-
-
Krishnan, A.1
Zbilut, J.P.2
Tomita, M.3
Giuliani, A.4
-
78
-
-
77955831624
-
Analysis and network representation of hotspots in protein interfaces using minimum cut trees
-
Tuncbag N., Salman F.S., Keskin O., Gursoy A. Analysis and network representation of hotspots in protein interfaces using minimum cut trees. Prot: Struct Funct Bioinform 2010, 78:2283-2294.
-
(2010)
Prot: Struct Funct Bioinform
, vol.78
, pp. 2283-2294
-
-
Tuncbag, N.1
Salman, F.S.2
Keskin, O.3
Gursoy, A.4
-
79
-
-
34249910312
-
Network analysis of protein dynamics
-
Böde C., Kovács I.A., Szalay M.S., Palotai R., Korcsmáros T., Csermely P. Network analysis of protein dynamics. FEBS Lett 2007, 581:2776-2782.
-
(2007)
FEBS Lett
, vol.581
, pp. 2776-2782
-
-
Böde, C.1
Kovács, I.A.2
Szalay, M.S.3
Palotai, R.4
Korcsmáros, T.5
Csermely, P.6
-
80
-
-
84861505274
-
Refining regulatory networks through phylogenetic transfer of information
-
Zhang X., Moret B.M.E. Refining regulatory networks through phylogenetic transfer of information. IEEE/ACM Trans Comput Biol Bioinform 2012, 9:1032-1045.
-
(2012)
IEEE/ACM Trans Comput Biol Bioinform
, vol.9
, pp. 1032-1045
-
-
Zhang, X.1
Moret, B.M.E.2
-
81
-
-
76949098494
-
Refining transcriptional regulatory networks using network evolutionary models and gene histories
-
Zhang X., Moret B.M.E. Refining transcriptional regulatory networks using network evolutionary models and gene histories. Algorith Mol Biol 2010, 5:1.
-
(2010)
Algorith Mol Biol
, vol.5
, pp. 1
-
-
Zhang, X.1
Moret, B.M.E.2
|