-
1
-
-
11244281311
-
The ‘evolvability’ of promiscuous protein functions
-
Aharoni, A, Gaidukov, L, Khersonsky, O, Mc, QGS, Roodveldt, C, and Tawfik, DS. 2005. “The ‘evolvability’ of promiscuous protein functions.”. Bull. Ninth Dist. Dent. Soc., 37:73–76.
-
(2005)
Bull. Ninth Dist. Dent. Soc.
, vol.37
, pp. 73-76
-
-
Aharoni, A.1
Gaidukov, L.2
Khersonsky, O.3
Mc, Q.G.S.4
Roodveldt, C.5
Tawfik, D.S.6
-
2
-
-
36749042777
-
Latent evolutionary potentials under the neutral mutational drift of an enzyme
-
Amitai, G, Gupta, R, and Tawfik, DS. 2007. “Latent evolutionary potentials under the neutral mutational drift of an enzyme.”. HFSP J., 1:67–78.
-
(2007)
HFSP J.
, vol.1
, pp. 67-78
-
-
Amitai, G.1
Gupta, R.2
Tawfik, D.S.3
-
3
-
-
0035252648
-
How enzymes adapt: Lessons from directed evolution
-
Arnold, FH, Wintrode, PL, Miyazaki, K, and Gershenson, A. 2001. “How enzymes adapt:lessons from directed evolution.”. Trends Biochem. Sci., 26:100–106.
-
(2001)
Trends Biochem. Sci.
, vol.26
, pp. 100-106
-
-
Arnold, F.H.1
Wintrode, P.L.2
Miyazaki, K.3
Gershenson, A.4
-
4
-
-
0033533517
-
Neutral evolution of model proteins: Diffusion in sequence space and overdispersion
-
Bastolla, U, Roman, HE, and Vendruscolo, M. 1999. “Neutral evolution of model proteins:diffusion in sequence space and overdispersion.”. J. Theor. Biol., 200:49–64.
-
(1999)
J. Theor. Biol.
, vol.200
, pp. 49-64
-
-
Bastolla, U.1
Roman, H.E.2
Vendruscolo, M.3
-
5
-
-
9144257886
-
The Pfam protein families database
-
Bateman, A. 2004. “The Pfam protein families database.”. Nucleic Acids Res., 32:D138–D1416.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. D138-D1416
-
-
Bateman, A.1
-
7
-
-
33645691679
-
Evolution of hormone-receptor complexity by molecular exploitation
-
Bridgham, JT, Carroll, SM, and Thornton, JW. 2006. “Evolution of hormone-receptor complexity by molecular exploitation.”. Science, 312:97–101.
-
(2006)
Science
, vol.312
, pp. 97-101
-
-
Bridgham, J.T.1
Carroll, S.M.2
Thornton, J.W.3
-
8
-
-
16844387465
-
The first steps in adaptive evolution
-
Bull, JJ, and Otto, SP. 2005. “The first steps in adaptive evolution.”. Nat. Genet., 37:342–343.
-
(2005)
Nat. Genet.
, vol.37
, pp. 342-343
-
-
Bull, J.J.1
Otto, S.P.2
-
10
-
-
84960286082
-
A structure-centric view of protein evolution, design, and adaptation
-
Deeds, EJ, and Shakhnovich, EI. 2007. “A structure-centric view of protein evolution, design, and adaptation.”. Adv. Enzymol. Relat. Areas Mol. Biol., 75:133–191.
-
(2007)
Adv. Enzymol. Relat. Areas Mol. Biol.
, vol.75
, pp. 133-191
-
-
Deeds, E.J.1
Shakhnovich, E.I.2
-
12
-
-
0038441327
-
Evolution experiments with microorganisms: The dynamics and genetic bases of adaptation
-
Elena, SF, and Lenski, RE. 2003. “Evolution experiments with microorganisms:the dynamics and genetic bases of adaptation.”. Nat. Rev. Genet., 4:457–469.
-
(2003)
Nat. Rev. Genet.
, vol.4
, pp. 457-469
-
-
Elena, S.F.1
Lenski, R.E.2
-
14
-
-
0032577365
-
Continuity in evolution: On the nature of transitions
-
Fontana, W, and Schuster, P. 1998. “Continuity in evolution:on the nature of transitions.”. Science, 280:1451–1455.
-
(1998)
Science
, vol.280
, pp. 1451-1455
-
-
Fontana, W.1
Schuster, P.2
-
15
-
-
0026320866
-
The energy landscapes and motions of proteins
-
Frauenfelder, H, Sligar, SG, and Wolynes, PG. 1991. “The energy landscapes and motions of proteins.”. Science, 254:1598–1603.
-
(1991)
Science
, vol.254
, pp. 1598-1603
-
-
Frauenfelder, H.1
Sligar, S.G.2
Wolynes, P.G.3
-
17
-
-
0346373759
-
Unifying the epidemiological and evolutionary dynamics of pathogens
-
Grenfell, BT, Pybus, OG, Gog, JR, Wood, JL, Daly, JM, Mumford, JA, and Holmes, EC. 2004. “Unifying the epidemiological and evolutionary dynamics of pathogens.”. Science, 303:327–332.
-
(2004)
Science
, vol.303
, pp. 327-332
-
-
Grenfell, B.T.1
Pybus, O.G.2
Gog, J.R.3
Wood, J.L.4
Daly, J.M.5
Mumford, J.A.6
Holmes, E.C.7
-
18
-
-
33748525883
-
Enzyme promiscuity: Evolutionary and mechanistic aspects
-
Khersonsky, O, Roodveldt, C, and Tawfik, DS. 2006. “Enzyme promiscuity:evolutionary and mechanistic aspects.”. Curr. Opin. Chem. Biol., 10:498–508.
-
(2006)
Curr. Opin. Chem. Biol.
, vol.10
, pp. 498-508
-
-
Khersonsky, O.1
Roodveldt, C.2
Tawfik, D.S.3
-
20
-
-
0016087667
-
On some principles governing molecular evolution
-
Kimura, M, and Ota, T. 1974. “On some principles governing molecular evolution.”. Proc. Natl. Acad. Sci. U.S.A., 71:2848–2852.
-
(1974)
Proc. Natl. Acad. Sci. U.S.A.
, vol.71
, pp. 2848-2852
-
-
Kimura, M.1
Ota, T.2
-
21
-
-
0029772552
-
Emergence of preferred structures in a simple model of protein folding
-
Li, H, Helling, R, Tang, C, and Wingreen, N. 1996. “Emergence of preferred structures in a simple model of protein folding.”. Science, 273:666–669.
-
(1996)
Science
, vol.273
, pp. 666-669
-
-
Li, H.1
Helling, R.2
Tang, C.3
Wingreen, N.4
-
22
-
-
27144538817
-
The biochemical architecture of an ancient adaptive landscape
-
Lunzer, M, Miller, SP, Felsheim, R, and Dean, AM. 2005. “The biochemical architecture of an ancient adaptive landscape.”. Science, 310:499–501.
-
(2005)
Science
, vol.310
, pp. 499-501
-
-
Lunzer, M.1
Miller, S.P.2
Felsheim, R.3
Dean, A.M.4
-
23
-
-
0345306751
-
The origins of genome complexity
-
Lynch, M, and Conery, JS. 2003. “The origins of genome complexity.”. Science, 302:1401–1404.
-
(2003)
Science
, vol.302
, pp. 1401-1404
-
-
Lynch, M.1
Conery, J.S.2
-
24
-
-
4744343021
-
The altered evolutionary trajectories of gene duplicates
-
Lynch, M, and Katju, V. 2004. “The altered evolutionary trajectories of gene duplicates.”. Trends Genet., 20:544–549.
-
(2004)
Trends Genet.
, vol.20
, pp. 544-549
-
-
Lynch, M.1
Katju, V.2
-
25
-
-
0035697435
-
The probability of preservation of a newly arisen gene duplicate
-
Lynch, M, O'Hely, M, Walsh, B, and Force, A. 2001. “The probability of preservation of a newly arisen gene duplicate.”. Genetics, 159:1789–1804.
-
(2001)
Genetics
, vol.159
, pp. 1789-1804
-
-
Lynch, M.1
O'Hely, M.2
Walsh, B.3
Force, A.4
-
26
-
-
0036737593
-
The emergence of resistance to targeted cancer therapeutics
-
Mellinghoff, IK, and Sawyers, CL. 2002. “The emergence of resistance to targeted cancer therapeutics.”. Pharmacogenomics, 3:603–623.
-
(2002)
Pharmacogenomics
, vol.3
, pp. 603-623
-
-
Mellinghoff, I.K.1
Sawyers, C.L.2
-
27
-
-
33750287639
-
Direct demonstration of an adaptive constraint
-
Miller, SP, Lunzer, M, and Dean, AM. 2006. “Direct demonstration of an adaptive constraint.”. Science, 314:458–461.
-
(2006)
Science
, vol.314
, pp. 458-461
-
-
Miller, S.P.1
Lunzer, M.2
Dean, A.M.3
-
29
-
-
0034707210
-
Evolution of gene families
-
Ohta, T. 2000. “Evolution of gene families.”. Gene, 259:45–52.
-
(2000)
Gene
, vol.259
, pp. 45-52
-
-
Ohta, T.1
-
30
-
-
0012088802
-
On the constancy of the evolutionary rate of cistrons
-
Ohta, T, and Kimura, M. 1972. “On the constancy of the evolutionary rate of cistrons.”. J. Mol. Biol., 1:305–314.
-
(1972)
J. Mol. Biol.
, vol.1
, pp. 305-314
-
-
Ohta, T.1
Kimura, M.2
-
31
-
-
13144257707
-
The genetic theory of adaptation: A brief history
-
Orr, AH. 2005. “The genetic theory of adaptation:a brief history.”. Nat. Rev. Genet., 6:119–127.
-
(2005)
Nat. Rev. Genet.
, vol.6
, pp. 119-127
-
-
Orr, A.H.1
-
32
-
-
0031714655
-
The population genetics of adaptation: The distribution of factors fixed during adaptive evolution
-
Orr, HA. 1998. “The population genetics of adaptation:the distribution of factors fixed during adaptive evolution.”. Evolution, 52:935–949.
-
(1998)
Evolution
, vol.52
, pp. 935-949
-
-
Orr, H.A.1
-
33
-
-
0037398394
-
The distribution of fitness effects among beneficial mutations
-
Orr, HA. 2003. “The distribution of fitness effects among beneficial mutations.”. Genetics, 163:1519–1526.
-
(2003)
Genetics
, vol.163
, pp. 1519-1526
-
-
Orr, H.A.1
-
34
-
-
33750273036
-
Protein superfamily evolution and the last universal common ancestor (LUCA)
-
Ranea, JA, Sillero, A, Thornton, JM, and Orengo, CA. 2006. “Protein superfamily evolution and the last universal common ancestor (LUCA).”. J. Mol. Evol., 63:513–525.
-
(2006)
J. Mol. Evol.
, vol.63
, pp. 513-525
-
-
Ranea, J.A.1
Sillero, A.2
Thornton, J.M.3
Orengo, C.A.4
-
35
-
-
0035912249
-
HIV chemotherapy
-
Richman, DD. 2001. “HIV chemotherapy.”. Nature, 410:995–1001.
-
(2001)
Nature
, vol.410
, pp. 995-1001
-
-
Richman, D.D.1
-
36
-
-
16844369125
-
An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus
-
Rokyta, DR, Joyce, P, Caudle, SB, and Wichman, HA. 2005. “An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus.”. Nat. Genet., 37:441–444.
-
(2005)
Nat. Genet.
, vol.37
, pp. 441-444
-
-
Rokyta, D.R.1
Joyce, P.2
Caudle, S.B.3
Wichman, H.A.4
-
37
-
-
0037780207
-
Evolutionary potential of (beta/alpha)8-barrels: Functional promiscuity produced by single substitutions in the enolase superfamily
-
Schmidt, DM, Mundorff, EC, Dojka, M, Bermudez, E, Ness, JE, Govindarajan, S, Babbitt, PC, Minshull, J, and Gerlt, JA. 2003. “Evolutionary potential of (beta/alpha)8-barrels:functional promiscuity produced by single substitutions in the enolase superfamily.”. Biochemistry, 42:8387–8393.
-
(2003)
Biochemistry
, vol.42
, pp. 8387-8393
-
-
Schmidt, D.M.1
Mundorff, E.C.2
Dojka, M.3
Bermudez, E.4
Ness, J.E.5
Govindarajan, S.6
Babbitt, P.C.7
Minshull, J.8
Gerlt, J.A.9
-
38
-
-
0035930008
-
The topology of the possible: Formal spaces underlying patterns of evolutionary change
-
Stadler, BM, Stadler, PF, Wagner, GP, and Fontana, W. 2001. “The topology of the possible:formal spaces underlying patterns of evolutionary change.”. J. Theor. Biol., 213:241–274.
-
(2001)
J. Theor. Biol.
, vol.213
, pp. 241-274
-
-
Stadler, B.M.1
Stadler, P.F.2
Wagner, G.P.3
Fontana, W.4
-
39
-
-
4744339316
-
Evolution of enzymes for the metabolism of new chemical inputs into the environment
-
Wackett, LP. 2004. “Evolution of enzymes for the metabolism of new chemical inputs into the environment.”. J. Biol. Chem., 279:41259–41262.
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 41259-41262
-
-
Wackett, L.P.1
-
41
-
-
0028893838
-
How often do duplicated genes evolve new functions?
-
Walsh, JB. 1995. “How often do duplicated genes evolve new functions?”. Genetics, 139:421–428.
-
(1995)
Genetics
, vol.139
, pp. 421-428
-
-
Walsh, J.B.1
-
42
-
-
33645666942
-
Darwinian evolution can follow only very few mutational paths to fitter proteins
-
Weinreich, DM, Delaney, NF, DePristo, MA, and Hartl, DL. 2006. “Darwinian evolution can follow only very few mutational paths to fitter proteins.”. Science, 312:111–114.
-
(2006)
Science
, vol.312
, pp. 111-114
-
-
Weinreich, D.M.1
Delaney, N.F.2
DePristo, M.A.3
Hartl, D.L.4
-
44
-
-
0023184331
-
Bacterial evolution
-
Woese, CR. 1987. “Bacterial evolution.”. FEMS Microbiol. Rev., 51:221–271.
-
(1987)
FEMS Microbiol. Rev.
, vol.51
, pp. 221-271
-
-
Woese, C.R.1
-
45
-
-
41649116075
-
A structural model of latent evolutionary potentials underlying neutral networks in proteins
-
Wroe, R, Chan, HS, and Bornberg-Bauer, E. 2007. “A structural model of latent evolutionary potentials underlying neutral networks in proteins.”. HFSP J., 1:79–87.
-
(2007)
HFSP J.
, vol.1
, pp. 79-87
-
-
Wroe, R.1
Chan, H.S.2
Bornberg-Bauer, E.3
-
46
-
-
2542529286
-
A new activity for an old enzyme: Escherichia coli bacterial alkaline phosphatase is a phosphitedependent hydrogenase
-
Yang, K, and Metcalf, WW. 2004. “A new activity for an old enzyme:Escherichia coli bacterial alkaline phosphatase is a phosphitedependent hydrogenase.”. Proc. Natl. Acad. Sci. U.S.A., 101:7919–7924.
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 7919-7924
-
-
Yang, K.1
Metcalf, W.W.2
-
47
-
-
14544286855
-
The selective cause of an ancient adaptation
-
Zhu, G, Golding, GB, and Dean, AM. 2005. “The selective cause of an ancient adaptation.”. Science, 307:1279–1282.
-
(2005)
Science
, vol.307
, pp. 1279-1282
-
-
Zhu, G.1
Golding, G.B.2
Dean, A.M.3
-
48
-
-
0001895697
-
Evolutionary divergence and convergence in proteins
-
Bryson V., Vogel H., (eds), New York: Academic
-
Zuckerkandl, E, and Pauling, L. 1965. “Evolutionary divergence and convergence in proteins.”. In Evolving Genes and Proteins, A Symposium, Edited by:Bryson, V, and Vogel, H. 97–166. New York:Academic.
-
(1965)
Evolving Genes and Proteins, A Symposium
, pp. 97-166
-
-
Zuckerkandl, E.1
Pauling, L.2
|