-
3
-
-
0033858110
-
From complete genomes to measures of substitution rate variability within and between proteins
-
Grishin NV, Wolf YI, Koonin EV (2000) From complete genomes to measures of substitution rate variability within and between proteins. Genome Res 10:991-1000.
-
(2000)
Genome Res
, vol.10
, pp. 991-1000
-
-
Grishin, N.V.1
Wolf, Y.I.2
Koonin, E.V.3
-
4
-
-
66149123308
-
Inaugural Article: The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages
-
Wolf YI, Novichkov PS, Karev GP, Koonin EV, Lipman DJ (2009) Inaugural Article: The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages. Proc Natl Acad Sci USA 106:7273-7280.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 7273-7280
-
-
Wolf, Y.I.1
Novichkov, P.S.2
Karev, G.P.3
Koonin, E.V.4
Lipman, D.J.5
-
5
-
-
0017227120
-
Evolutionary processes and evolutionary noise at the molecular level. I. Functional density in proteins
-
Zuckerkandl E (1976) Evolutionary processes and evolutionary noise at the molecular level. I. Functional density in proteins. J Mol Evol 7:167-183.
-
(1976)
J Mol Evol
, vol.7
, pp. 167-183
-
-
Zuckerkandl, E.1
-
7
-
-
33748980210
-
Evolutionary systems biology: Links between gene evolution and function
-
Koonin EV, Wolf YI (2006) Evolutionary systems biology: Links between gene evolution and function. Curr Opin Biotechnol 17:481-487.
-
(2006)
Curr Opin Biotechnol
, vol.17
, pp. 481-487
-
-
Koonin, E.V.1
Wolf, Y.I.2
-
8
-
-
33746192317
-
Unifying measures of gene function and evolution
-
Wolf YI, Carmel L, Koonin EV (2006) Unifying measures of gene function and evolution. Proc Biol Sci 273:1507-1515.
-
(2006)
Proc Biol Sci
, vol.273
, pp. 1507-1515
-
-
Wolf, Y.I.1
Carmel, L.2
Koonin, E.V.3
-
9
-
-
33646182934
-
An integrated view of protein evolution
-
Pál C, Papp B, Lercher MJ (2006) An integrated view of protein evolution. Nat Rev Genet 7:337-348.
-
(2006)
Nat Rev Genet
, vol.7
, pp. 337-348
-
-
Pál, C.1
Papp, B.2
Lercher, M.J.3
-
10
-
-
33646375934
-
The causes of protein evolutionary rate variation
-
McInerney JO (2006) The causes of protein evolutionary rate variation. Trends Ecol Evol 21:230-232.
-
(2006)
Trends Ecol Evol
, vol.21
, pp. 230-232
-
-
McInerney, J.O.1
-
11
-
-
0034978556
-
Highly expressed genes in yeast evolve slowly
-
Pál C, Papp B, Hurst LD (2001) Highly expressed genes in yeast evolve slowly. Genetics 158:927-931.
-
(2001)
Genetics
, vol.158
, pp. 927-931
-
-
Pál, C.1
Papp, B.2
Hurst, L.D.3
-
12
-
-
0142124263
-
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
-
Krylov DM, Wolf YI, Rogozin IB, Koonin EV (2003) Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res 13:2229-2235.
-
(2003)
Genome Res
, vol.13
, pp. 2229-2235
-
-
Krylov, D.M.1
Wolf, Y.I.2
Rogozin, I.B.3
Koonin, E.V.4
-
13
-
-
26444621352
-
Why highly expressed proteins evolve slowly
-
Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH (2005) Why highly expressed proteins evolve slowly. Proc Natl Acad Sci USA 102:14338-14343.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 14338-14343
-
-
Drummond, D.A.1
Bloom, J.D.2
Adami, C.3
Wilke, C.O.4
Arnold, F.H.5
-
14
-
-
30744441602
-
A single determinant dominates the rate of yeast protein evolution
-
Drummond DA, Raval A, Wilke CO (2006) A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol 23:327-337.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 327-337
-
-
Drummond, D.A.1
Raval, A.2
Wilke, C.O.3
-
15
-
-
47549097539
-
Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
-
Drummond DA, Wilke CO (2008) Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134:341-352.
-
(2008)
Cell
, vol.134
, pp. 341-352
-
-
Drummond, D.A.1
Wilke, C.O.2
-
16
-
-
70349333227
-
The evolutionary consequences of erroneous protein synthesis
-
Drummond DA, Wilke CO (2009) The evolutionary consequences of erroneous protein synthesis. Nat Rev Genet 10:715-724.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 715-724
-
-
Drummond, D.A.1
Wilke, C.O.2
-
17
-
-
0028929556
-
Principles of protein folding-a perspective from simple exact models
-
Dill KA, et al. (1995) Principles of protein folding-a perspective from simple exact models. Protein Sci 4:561-602.
-
(1995)
Protein Sci
, vol.4
, pp. 561-602
-
-
Dill, K.A.1
-
19
-
-
33646931471
-
Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet
-
Shakhnovich E (2006) Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet. Chem Rev 106:1559-1588.
-
(2006)
Chem Rev
, vol.106
, pp. 1559-1588
-
-
Shakhnovich, E.1
-
20
-
-
1842839788
-
Simulating protein evolution in sequence and structure space
-
Xia Y, Levitt M (2004) Simulating protein evolution in sequence and structure space. Curr Opin Struct Biol 14:202-207.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 202-207
-
-
Xia, Y.1
Levitt, M.2
-
21
-
-
0036340797
-
Randomness, structural uniqueness, modularity and neutral evolution in sequence space of model proteins
-
Bornberg-Bauer E (2002) Randomness, structural uniqueness, modularity and neutral evolution in sequence space of model proteins. Z Phys Chem 216:139-154.
-
(2002)
Z Phys Chem
, vol.216
, pp. 139-154
-
-
Bornberg-Bauer, E.1
-
22
-
-
0033117927
-
Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models
-
Thirumalai D, Klimov DK (1999) Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models. Curr Opin Struct Biol 9:197-207.
-
(1999)
Curr Opin Struct Biol
, vol.9
, pp. 197-207
-
-
Thirumalai, D.1
Klimov, D.K.2
-
23
-
-
39149100599
-
Coarse-grained models of protein folding: Toy models or predictive tools?
-
Clementi C (2008) Coarse-grained models of protein folding: Toy models or predictive tools? Curr Opin Struct Biol 18:10-15.
-
(2008)
Curr Opin Struct Biol
, vol.18
, pp. 10-15
-
-
Clementi, C.1
-
24
-
-
0000533961
-
Folding, design, and determination of interaction potentials using off-lattice dynamics of model heteropolymers
-
Clementi C, Maritan A, Banavar JR (1998) Folding, design, and determination of interaction potentials using off-lattice dynamics of model heteropolymers. Phys Rev Lett 81:3287-3290.
-
(1998)
Phys Rev Lett
, vol.81
, pp. 3287-3290
-
-
Clementi, C.1
Maritan, A.2
Banavar, J.R.3
-
25
-
-
0032169011
-
Proposed mechanism for stability of proteins to evolutionary mutations
-
Nelson ED, Onuchic JN (1998) Proposed mechanism for stability of proteins to evolutionary mutations. Proc Natl Acad Sci USA 95:10682-10686.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 10682-10686
-
-
Nelson, E.D.1
Onuchic, J.N.2
-
26
-
-
0001720011
-
Molecular dynamics of folding of secondary structures in Go-type models of proteins
-
Hoang TX, Cieplak M (2000) Molecular dynamics of folding of secondary structures in Go-type models of proteins. J Chem Phys 112:6851-6862.
-
(2000)
J Chem Phys
, vol.112
, pp. 6851-6862
-
-
Hoang, T.X.1
Cieplak, M.2
-
27
-
-
0036606863
-
Emergence of highly designable protein-backbone conformations in an off-lattice model
-
Miller J, Zeng C, Wingreen NS, Tang C (2002) Emergence of highly designable protein-backbone conformations in an off-lattice model. Proteins 47:506-512.
-
(2002)
Proteins
, vol.47
, pp. 506-512
-
-
Miller, J.1
Zeng, C.2
Wingreen, N.S.3
Tang, C.4
-
28
-
-
0346492908
-
Designability and thermal stability of protein structures
-
Wingreen NS, Li H, Tang C (2004) Designability and thermal stability of protein structures. Polymer 45:699-705.
-
(2004)
Polymer
, vol.45
, pp. 699-705
-
-
Wingreen, N.S.1
Li, H.2
Tang, C.3
-
29
-
-
33947322346
-
Identification of characteristic protein folding channels in a coarse-grained hydrophobic-polar peptide model
-
Schnabel S, Bachmann M, Janke W (2007) Identification of characteristic protein folding channels in a coarse-grained hydrophobic-polar peptide model. J Chem Phys 126:105102.
-
(2007)
J Chem Phys
, vol.126
, pp. 105102
-
-
Schnabel, S.1
Bachmann, M.2
Janke, W.3
-
30
-
-
13044269058
-
Modeling evolutionary landscapes: Mutational stability, topology, and superfunnels in sequence space
-
Bornberg-Bauer E, Chan HS (1999) Modeling evolutionary landscapes: Mutational stability, topology, and superfunnels in sequence space. Proc Natl Acad Sci USA 96: 10689-10694.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 10689-10694
-
-
Bornberg-Bauer, E.1
Chan, H.S.2
-
31
-
-
0030782481
-
How are model protein structures distributed in sequence space?
-
Bornberg-Bauer E (1997) How are model protein structures distributed in sequence space? Biophys J 73:2394-2403.
-
(1997)
Biophys J
, vol.73
, pp. 2394-2403
-
-
Bornberg-Bauer, E.1
-
32
-
-
22144437325
-
The application of statistical physics to evolutionary biology
-
Sella G, Hirsh AE (2005) The application of statistical physics to evolutionary biology. Proc Natl Acad Sci USA 102:9541-9546.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 9541-9546
-
-
Sella, G.1
Hirsh, A.E.2
-
33
-
-
77649257256
-
-
LynchM, SinauerAssociates, Sunderland,MA
-
LynchM(2007) TheOriginsofGenome Architecture (SinauerAssociates, Sunderland,MA).
-
(2007)
TheOriginsofGenome Architecture
-
-
-
35
-
-
33645941402
-
The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin
-
Jorgensen WL, Tirado-Rives J (1988) The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J AmChemSoc 110:1657-1666.
-
(1988)
J AmChemSoc
, vol.110
, pp. 1657-1666
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
36
-
-
0033117763
-
Matching theory and experiment in protein folding
-
Alm E, Baker D (1999) Matching theory and experiment in protein folding. Curr Opin Struct Biol 9:189-196.
-
(1999)
Curr Opin Struct Biol
, vol.9
, pp. 189-196
-
-
Alm, E.1
Baker, D.2
-
38
-
-
0037292462
-
Study of the dynamics of protein folding through minimalistic models
-
Srinivas G, Bagchi B (2003) Study of the dynamics of protein folding through minimalistic models. Theor Chem Acc 109:8-21.
-
(2003)
Theor Chem Acc
, vol.109
, pp. 8-21
-
-
Srinivas, G.1
Bagchi, B.2
-
40
-
-
22544446147
-
Balancing energy and entropy: A minimalist model for the characterization of protein folding landscapes
-
Das P, Matysiak S, Clementi C (2005) Balancing energy and entropy: A minimalist model for the characterization of protein folding landscapes. Proc Natl Acad Sci USA 102:10141-10146.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 10141-10146
-
-
Das, P.1
Matysiak, S.2
Clementi, C.3
-
41
-
-
0031465967
-
New view of protein folding reconciled with the old through multiple unfolding simulations
-
Lazaridis T, Karplus M (1997) "New view" of protein folding reconciled with the old through multiple unfolding simulations. Science 278:1928-1931.
-
(1997)
Science
, vol.278
, pp. 1928-1931
-
-
Lazaridis, T.1
Karplus, M.2
-
42
-
-
33748770940
-
Minimalist protein model as a diagnostic tool for misfolding and aggregation
-
Matysiak S, Clementi C (2006) Minimalist protein model as a diagnostic tool for misfolding and aggregation. J Mol Biol 363:297-308.
-
(2006)
J Mol Biol
, vol.363
, pp. 297-308
-
-
Matysiak, S.1
Clementi, C.2
-
43
-
-
26844543506
-
Characterization of the folding landscape of monomeric lactose repressor: Quantitative comparison of theory and experiment
-
Das P, et al. (2005) Characterization of the folding landscape of monomeric lactose repressor: Quantitative comparison of theory and experiment. Proc Natl Acad Sci USA 102:14569-14574.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 14569-14574
-
-
Das, P.1
-
44
-
-
0034224554
-
Folding path in a semiflexible homopolymer chain: A brownian dynamics simulation
-
Noguchi H, Yoshikawa K (2000) Folding path in a semiflexible homopolymer chain: A brownian dynamics simulation. J Chem Phys 113:854-862.
-
(2000)
J Chem Phys
, vol.113
, pp. 854-862
-
-
Noguchi, H.1
Yoshikawa, K.2
-
45
-
-
0015859467
-
Principles that govern the folding of protein chains
-
Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181: 223-230.
-
(1973)
Science
, vol.181
, pp. 223-230
-
-
Anfinsen, C.B.1
-
46
-
-
0025368288
-
Metastability of the folded states of globular proteins
-
Honeycutt JD, Thirumalai D (1990) Metastability of the folded states of globular proteins. Proc Natl Acad Sci USA 87:3526-3529.
-
(1990)
Proc Natl Acad Sci USA
, vol.87
, pp. 3526-3529
-
-
Honeycutt, J.D.1
Thirumalai, D.2
-
47
-
-
0032510675
-
On the thermodynamic hypothesis of protein folding
-
Govindarajan S, Goldstein RA (1998) On the thermodynamic hypothesis of protein folding. Proc Natl Acad Sci USA 95:5545-5549.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 5545-5549
-
-
Govindarajan, S.1
Goldstein, R.A.2
-
48
-
-
36248963478
-
-
Cambridge Univ Press, Cambridge, UK, 1st Ed, pp
-
Press WH, Flannery BP, Teukolsky SA, Vettering WT (1986) Combinatorial Minimization: Method of Simulated Annealing (Cambridge Univ Press, Cambridge, UK), 1st Ed, pp 326-334.
-
(1986)
Combinatorial Minimization: Method of Simulated Annealing
, pp. 326-334
-
-
Press, W.H.1
Flannery, B.P.2
Teukolsky, S.A.3
Vettering, W.T.4
-
49
-
-
36049027813
-
Protein stability imposes limits on organism complexity and speed of molecular evolution
-
Zeldovich KB, Chen P, Shakhnovich EI (2007) Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc Natl Acad Sci USA 104: 16152-16157.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 16152-16157
-
-
Zeldovich, K.B.1
Chen, P.2
Shakhnovich, E.I.3
-
50
-
-
0000713579
-
Designability, thermodynamic stability, and dynamics in protein folding: A lattice model study
-
Mélin R, Li H, Wingreen NS, Tang C (1999) Designability, thermodynamic stability, and dynamics in protein folding: A lattice model study. J Chem Phys 110:1252-1262.
-
(1999)
J Chem Phys
, vol.110
, pp. 1252-1262
-
-
Mélin, R.1
Li, H.2
Wingreen, N.S.3
Tang, C.4
-
51
-
-
0037154157
-
Recombinatoric exploration of novel folded structures: A heteropolymer-based model of protein evolutionary landscapes
-
Cui Y, Wong WH, Bornberg-Bauer E, Chan HS (2002) Recombinatoric exploration of novel folded structures: A heteropolymer-based model of protein evolutionary landscapes. Proc Natl Acad Sci USA 99:809-814.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 809-814
-
-
Cui, Y.1
Wong, W.H.2
Bornberg-Bauer, E.3
Chan, H.S.4
-
52
-
-
0030691734
-
Evolution of model proteins on a foldability landscape
-
Govindarajan S, Goldstein RA (1997) Evolution of model proteins on a foldability landscape. Proteins 29:461-466.
-
(1997)
Proteins
, vol.29
, pp. 461-466
-
-
Govindarajan, S.1
Goldstein, R.A.2
-
54
-
-
0030831997
-
Evolution of the folding ability of proteins through functional selection
-
Saito S, Sasai M, Yomo T (1997) Evolution of the folding ability of proteins through functional selection. Proc Natl Acad Sci USA 94:11324-11328.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 11324-11328
-
-
Saito, S.1
Sasai, M.2
Yomo, T.3
-
55
-
-
1842835981
-
Stability and the evolvability of function in a model protein
-
Bloom JD, Wilke CO, Arnold FH, Adami C (2004) Stability and the evolvability of function in a model protein. Biophys J 86:2758-2764.
-
(2004)
Biophys J
, vol.86
, pp. 2758-2764
-
-
Bloom, J.D.1
Wilke, C.O.2
Arnold, F.H.3
Adami, C.4
-
56
-
-
33646904645
-
Population genetics of translational robustness
-
Wilke CO, Drummond DA (2006) Population genetics of translational robustness. Genetics 173:473-481.
-
(2006)
Genetics
, vol.173
, pp. 473-481
-
-
Wilke, C.O.1
Drummond, D.A.2
-
58
-
-
65949096636
-
-
Schrimpf SP, et al. (2009) Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biol 7:e1000048.
-
Schrimpf SP, et al. (2009) Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biol 7:e1000048.
-
-
-
-
59
-
-
54949151498
-
Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution
-
Wolf MY, Wolf YI, Koonin EV (2008) Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution. Biol Direct 3:40.
-
(2008)
Biol Direct
, vol.3
, pp. 40
-
-
Wolf, M.Y.1
Wolf, Y.I.2
Koonin, E.V.3
-
60
-
-
36749113806
-
Brownian dynamics: Its applications to ionic solutions
-
Turq P, Lantelme F, Friedman HL (1977) Brownian dynamics: Its applications to ionic solutions. J Chem Phys 66:3039-3044.
-
(1977)
J Chem Phys
, vol.66
, pp. 3039-3044
-
-
Turq, P.1
Lantelme, F.2
Friedman, H.L.3
-
61
-
-
0030660581
-
A genomic perspective on protein families
-
Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278:631-637.
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
62
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
63
-
-
0029901637
-
Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods
-
Felsenstein J (1996) Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol 266:418-427.
-
(1996)
Methods Enzymol
, vol.266
, pp. 418-427
-
-
Felsenstein, J.1
-
64
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275-282.
-
(1992)
Comput Appl Biosci
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
|