-
1
-
-
0016355478
-
A new look at the statistical model identification
-
Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Automatic Control. 19:716-723.
-
(1974)
IEEE Trans Automatic Control.
, vol.19
, pp. 716-723
-
-
Akaike, H.1
-
2
-
-
84890067204
-
Protein evolution along phylogenetic histories under structurally constrained substitution models
-
Arenas M, Dos Santos HG, Posada D, Bastolla U. 2013. Protein evolution along phylogenetic histories under structurally constrained substitution models. Bioinformatics 29:3020-3028.
-
(2013)
Bioinformatics
, vol.29
, pp. 3020-3028
-
-
Arenas, M.1
Dos Santos, H.G.2
Posada, D.3
Bastolla, U.4
-
3
-
-
0030625954
-
Neutral networks in protein space: A computational study based on knowledge-based potentials of mean force
-
Babajide A, Hofacker IL, Sippl MJ, Stadler PF. 1997. Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force. Fold Des. 2:261-269.
-
(1997)
Fold Des.
, vol.2
, pp. 261-269
-
-
Babajide, A.1
Hofacker, I.L.2
Sippl, M.J.3
Stadler, P.F.4
-
4
-
-
0035427382
-
How to guarantee optimal stability for most representative structures in the Protein Data Bank
-
Bastolla U, Farwer J, Knapp EW, VendruscoloM. 2001. How to guarantee optimal stability for most representative structures in the Protein Data Bank. Proteins 44:79-96.
-
(2001)
Proteins
, vol.44
, pp. 79-96
-
-
Bastolla, U.1
Farwer, J.2
Knapp, E.W.3
Vendruscolo, M.4
-
5
-
-
6344282274
-
Genomic determinants of protein folding thermodynamics in prokaryotic organisms
-
Bastolla U, Moya A, Viguera E, van Ham RC. 2004. Genomic determinants of protein folding thermodynamics in prokaryotic organisms. J Mol Biol. 343:1451-1466.
-
(2004)
J Mol Biol.
, vol.343
, pp. 1451-1466
-
-
Bastolla, U.1
Moya, A.2
Viguera, E.3
Van Ham, R.C.4
-
6
-
-
58149292218
-
Effective connectivity profile: A structural representation that evidences the relationship between protein structures and sequences
-
Bastolla U, Ortiz AR, Porto M, Teichert F. 2008. Effective connectivity profile: a structural representation that evidences the relationship between protein structures and sequences. Proteins 73:872-888.
-
(2008)
Proteins
, vol.73
, pp. 872-888
-
-
Bastolla, U.1
Ortiz, A.R.2
Porto, M.3
Teichert, F.4
-
7
-
-
0346750651
-
Statistical properties of neutral evolution
-
Bastolla U, Porto M, Roman HE, Vendruscolo M. 2003. Statistical properties of neutral evolution. J Mol Evol. 57(Suppl 1), S103-S119.
-
(2003)
J Mol Evol.
, vol.57
, pp. S103-S119
-
-
Bastolla, U.1
Porto, M.2
Roman, H.E.3
Vendruscolo, M.4
-
8
-
-
10844225367
-
Principal eigenvector of contact matrices and hydrophobicity profiles in proteins
-
Bastolla U, Porto M, Roman HE, Vendruscolo M. 2005. Principal eigenvector of contact matrices and hydrophobicity profiles in proteins. Proteins 58:22-30.
-
(2005)
Proteins
, vol.58
, pp. 22-30
-
-
Bastolla, U.1
Porto, M.2
Roman, H.E.3
Vendruscolo, M.4
-
9
-
-
33748925566
-
A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank
-
Bastolla U, Porto M, Roman HE, Vendruscolo M. 2006. A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank. BMC Evol Biol. 6:43.
-
(2006)
BMC Evol Biol.
, vol.6
, pp. 43
-
-
Bastolla, U.1
Porto, M.2
Roman, H.E.3
Vendruscolo, M.4
-
10
-
-
0033533517
-
Neutral evolution of model proteins: Diffusion in sequence space and overdispersion
-
Bastolla U, Roman HE, VendruscoloM. 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
-
11
-
-
33845503073
-
Adaptive evolution of transcription factor binding sites
-
Berg J, Willmann S, Lässig M. 2004. Adaptive evolution of transcription factor binding sites. BMC Evol Biol. 4:42.
-
(2004)
BMC Evol Biol.
, vol.4
, pp. 42
-
-
Berg, J.1
Willmann, S.2
Lässig, M.3
-
12
-
-
14144251690
-
Thermodynamic prediction of protein neutrality
-
Bloom JD, Silberg JJ, Wilke CO, Drummond DA, Adami C, Arnold FH. 2005. Thermodynamic prediction of protein neutrality. Proc Natl Acad Sci U S A. 102:606-611.
-
(2005)
Proc Natl Acad Sci U S A.
, vol.102
, pp. 606-611
-
-
Bloom, J.D.1
Silberg, J.J.2
Wilke, C.O.3
Drummond, D.A.4
Adami, C.5
Arnold, F.H.6
-
13
-
-
84895752277
-
A new formulation of protein evolutionary models that account for structural constraints
-
Bordner AJ, Mittelmann HD. 2014. A new formulation of protein evolutionary models that account for structural constraints. Mol Biol Evol. 31:736-749.
-
(2014)
Mol Biol Evol.
, vol.31
, pp. 736-749
-
-
Bordner, A.J.1
Mittelmann, H.D.2
-
14
-
-
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 U S A. 96:10689-10694.
-
(1999)
Proc Natl Acad Sci U S A.
, vol.96
, pp. 10689-10694
-
-
Bornberg-Bauer, E.1
Chan, H.S.2
-
15
-
-
0028947257
-
Funnels, pathways, and the energy landscape of protein folding: A synthesis
-
Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG. 1995. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins 21:167-195.
-
(1995)
Proteins
, vol.21
, pp. 167-195
-
-
Bryngelson, J.D.1
Onuchic, J.N.2
Socci, N.D.3
Wolynes, P.G.4
-
17
-
-
79953747234
-
Cooperativity, localnonlocal coupling, and nonnative interactions: Principles of protein folding from coarse-grained models
-
Chan HS, Zhang Z, Wallin S, Liu Z. 2011. Cooperativity, localnonlocal coupling, and nonnative interactions: principles of protein folding from coarse-grained models. Annu Rev Phys Chem. 62: 301-326.
-
(2011)
Annu Rev Phys Chem.
, vol.62
, pp. 301-326
-
-
Chan, H.S.1
Zhang, Z.2
Wallin, S.3
Liu, Z.4
-
18
-
-
23944490117
-
Missense meanderings in sequence space: A biophysical view of protein evolution
-
DePristo MA, Weinreich DM, Hartl DL. 2005. Missense meanderings in sequence space: a biophysical view of protein evolution. Nat Rev Genet. 6:678-687.
-
(2005)
Nat Rev Genet.
, vol.6
, pp. 678-687
-
-
DePristo, M.A.1
Weinreich, D.M.2
Hartl, D.L.3
-
19
-
-
4243861085
-
Random energy model: An exactly solvable model of disordered systems
-
Derrida B. 1981. Random energy model: an exactly solvable model of disordered systems. Phys Rev B. 24:2613-2626.
-
(1981)
Phys Rev B.
, vol.24
, pp. 2613-2626
-
-
Derrida, B.1
-
20
-
-
0035823119
-
Understanding hierarchical protein evolution from first principles
-
Dokholyan NV, Shakhnovich EI. 2001. Understanding hierarchical protein evolution from first principles. J Mol Biol. 312:289-307.
-
(2001)
J Mol Biol.
, vol.312
, pp. 289-307
-
-
Dokholyan, N.V.1
Shakhnovich, E.I.2
-
21
-
-
84959848780
-
Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters
-
Felsenstein J. 1973. Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Syst Zool. 22:240-249.
-
(1973)
Syst Zool.
, vol.22
, pp. 240-249
-
-
Felsenstein, J.1
-
23
-
-
0036184351
-
Site-specific amino acid replacement matrices from structurally constrained protein evolution simulations
-
Fornasari MS, Parisi G, Echave J. 2002. Site-specific amino acid replacement matrices from structurally constrained protein evolution simulations. Mol Biol Evol. 19:352-356.
-
(2002)
Mol Biol Evol.
, vol.19
, pp. 352-356
-
-
Fornasari, M.S.1
Parisi, G.2
Echave, J.3
-
24
-
-
70349911882
-
Structural determinants of protein evolution are context-sensitive at the residue level
-
Franzosa EA, Xia Y. 2009. Structural determinants of protein evolution are context-sensitive at the residue level. Mol Biol Evol. 26: 2387-2395.
-
(2009)
Mol Biol Evol.
, vol.26
, pp. 2387-2395
-
-
Franzosa, E.A.1
Xia, Y.2
-
25
-
-
84956127383
-
Mean-field model for protein folding
-
Garel T, Orland H. 1988. Mean-field model for protein folding. Europhys Lett. 6:307-310.
-
(1988)
Europhys Lett.
, vol.6
, pp. 307-310
-
-
Garel, T.1
Orland, H.2
-
26
-
-
79954542203
-
The evolution and evolutionary consequences of marginal thermostability in proteins
-
Goldstein RA. 2011. The evolution and evolutionary consequences of marginal thermostability in proteins. Proteins 79:1396-1407.
-
(2011)
Proteins
, vol.79
, pp. 1396-1407
-
-
Goldstein, R.A.1
-
27
-
-
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
-
30
-
-
0031875569
-
Evolutionary distances for protein-coding sequences: Modeling site-specific residue frequencies
-
Halpern AL, Bruno WJ. 1998. Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. Mol Biol Evol. 15:910-917.
-
(1998)
Mol Biol Evol.
, vol.15
, pp. 910-917
-
-
Halpern, A.L.1
Bruno, W.J.2
-
31
-
-
84899480289
-
A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility
-
Huang TT, del Valle Marcos ML, Hwang JK, Echave J. 2014. A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility. BMC Evol Biol. 14:78.
-
(2014)
BMC Evol Biol.
, vol.14
, pp. 78
-
-
Huang, T.T.1
Del Valle Marcos, M.L.2
Hwang, J.K.3
Echave, J.4
-
32
-
-
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
-
33
-
-
0023475026
-
Configurational entropy of native proteins
-
Karplus M, Ichiye T, Pettitt BM. 1987. Configurational entropy of native proteins. Biophys J. 52:1083-1085.
-
(1987)
Biophys J.
, vol.52
, pp. 1083-1085
-
-
Karplus, M.1
Ichiye, T.2
Pettitt, B.M.3
-
34
-
-
84875619226
-
MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
-
Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30:772-780.
-
(2013)
Mol Biol Evol.
, vol.30
, pp. 772-780
-
-
Katoh, K.1
Standley, D.M.2
-
35
-
-
0032529584
-
Models of natural mutations including site heterogeneity
-
Koshi JM, Goldstein RA. 1998. Models of natural mutations including site heterogeneity. Proteins 32:289-295.
-
(1998)
Proteins
, vol.32
, pp. 289-295
-
-
Koshi, J.M.1
Goldstein, R.A.2
-
36
-
-
0035221408
-
Analyzing site heterogeneity during protein evolution
-
Koshi JM, Goldstein RA. 2001. Analyzing site heterogeneity during protein evolution. Pac Symp Biocomput. 191-202.
-
(2001)
Pac Symp Biocomput.
, pp. 191-202
-
-
Koshi, J.M.1
Goldstein, R.A.2
-
37
-
-
0033026624
-
Using physical-chemistrybased substitution models in phylogenetic analyses of HIV-1 subtypes
-
Koshi JM, Mindell DP, Goldstein RA. 1999. Using physical-chemistrybased substitution models in phylogenetic analyses of HIV-1 subtypes. Mol Biol Evol. 16:173-179.
-
(1999)
Mol Biol Evol.
, vol.16
, pp. 173-179
-
-
Koshi, J.M.1
Mindell, D.P.2
Goldstein, R.A.3
-
38
-
-
2442691520
-
A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
-
Lartillot N, Philippe H. 2004. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol. 21:1095-1109.
-
(2004)
Mol Biol Evol.
, vol.21
, pp. 1095-1109
-
-
Lartillot, N.1
Philippe, H.2
-
39
-
-
84861434946
-
The interface of protein structure, protein biophysics, and molecular evolution
-
Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, et al. 2012. The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci. 21:769-785.
-
(2012)
Protein Sci.
, vol.21
, pp. 769-785
-
-
Liberles, D.A.1
Teichmann, S.A.2
Bahar, I.3
Bastolla, U.4
Bloom, J.5
Bornberg-Bauer, E.6
Colwell, L.J.7
De Koning, A.P.8
Dokholyan, N.V.9
Echave, J.10
-
40
-
-
77955013698
-
Mutation bias favors protein folding stability in the evolution of small populations
-
Mendez R, Fritsche M, Porto M, Bastolla U. 2010. Mutation bias favors protein folding stability in the evolution of small populations. PLoS Comput Biol. 6:e1000767.
-
(2010)
PLoS Comput Biol.
, vol.6
-
-
Mendez, R.1
Fritsche, M.2
Porto, M.3
Bastolla, U.4
-
41
-
-
84879410603
-
Detecting selection for negative design in proteins through an improved model of the misfolded state
-
Minning J, Porto M, Bastolla U. 2013. Detecting selection for negative design in proteins through an improved model of the misfolded state. Proteins 81:1102-1112.
-
(2013)
Proteins
, vol.81
, pp. 1102-1112
-
-
Minning, J.1
Porto, M.2
Bastolla, U.3
-
43
-
-
0035028705
-
Structural constraints and emergence of sequence patterns in protein evolution
-
Parisi G, Echave J. 2001. Structural constraints and emergence of sequence patterns in protein evolution. Mol Biol Evol. 18:750-756.
-
(2001)
Mol Biol Evol.
, vol.18
, pp. 750-756
-
-
Parisi, G.1
Echave, J.2
-
44
-
-
0036706015
-
Understanding protein folding with energy landscape theory. Part II: Quantitative aspects
-
Plotkin SS, Onuchic JN. 2002. Understanding protein folding with energy landscape theory. Part II: quantitative aspects. Q Rev Biophys. 35: 205-286.
-
(2002)
Q Rev Biophys.
, vol.35
, pp. 205-286
-
-
Plotkin, S.S.1
Onuchic, J.N.2
-
45
-
-
14544272929
-
Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences
-
Porto M, Roman HE, Vendruscolo M, Bastolla U. 2005. Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences. Mol Biol Evol. 22: 630-638.
-
(2005)
Mol Biol Evol.
, vol.22
, pp. 630-638
-
-
Porto, M.1
Roman, H.E.2
Vendruscolo, M.3
Bastolla, U.4
-
46
-
-
84858077472
-
The Pfam protein families database
-
Punta M, Coggill PC, Eberhardt RY,Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, et al. 2012. The Pfam protein families database. Nucleic Acids Res. 40:D290-D301.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D290-D301
-
-
Punta, M.1
Coggill, P.C.2
Eberhardt, R.Y.3
Mistry, J.4
Tate, J.5
Boursnell, C.6
Pang, N.7
Forslund, K.8
Ceric, G.9
Clements, J.10
-
47
-
-
1542642309
-
Protein evolution with dependence among codons due to tertiary structure
-
Robinson DM, Jones DT, Kishino H, Goldman N, Thorne JL. 2003. Protein evolution with dependence among codons due to tertiary structure. Mol Biol Evol. 20:1692-1704.
-
(2003)
Mol Biol Evol.
, vol.20
, pp. 1692-1704
-
-
Robinson, D.M.1
Jones, D.T.2
Kishino, H.3
Goldman, N.4
Thorne, J.L.5
-
48
-
-
15544374861
-
Site interdependence attributed to tertiary structure in amino acid sequence evolution
-
Rodrigue N, Lartillot N, Bryant D, Philippe H. 2005. Site interdependence attributed to tertiary structure in amino acid sequence evolution. Gene 347:207-217.
-
(2005)
Gene
, vol.347
, pp. 207-217
-
-
Rodrigue, N.1
Lartillot, N.2
Bryant, D.3
Philippe, H.4
-
49
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406-425.
-
(1987)
Mol Biol Evol.
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
50
-
-
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 U S A. 102:9541-9546.
-
(2005)
Proc Natl Acad Sci U S A.
, vol.102
, pp. 9541-9546
-
-
Sella, G.1
Hirsh, A.E.2
-
51
-
-
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
-
52
-
-
0024357911
-
Formation of unique structure in polypeptide chains
-
Shakhnovich EI, Gutin AM. 1989. Formation of unique structure in polypeptide chains. Biophys Chem. 34:187-199.
-
(1989)
Biophys Chem.
, vol.34
, pp. 187-199
-
-
Shakhnovich, E.I.1
Gutin, A.M.2
-
53
-
-
0036139093
-
Why are proteins marginally stable?
-
Taverna DM, Goldstein RA. 2002. Why are proteins marginally stable? Proteins 46:105-109.
-
(2002)
Proteins
, vol.46
, pp. 105-109
-
-
Taverna, D.M.1
Goldstein, R.A.2
-
54
-
-
0000766263
-
Folding and misfolding of designed proteinlike chains with mutations
-
Tiana G, Broglia RA, Roman HE, Vigezzi E, Shakhnovich EI. 1998. Folding and misfolding of designed proteinlike chains with mutations. J Chem Phys. 108:757-761.
-
(1998)
J Chem Phys.
, vol.108
, pp. 757-761
-
-
Tiana, G.1
Broglia, R.A.2
Roman, H.E.3
Vigezzi, E.4
Shakhnovich, E.I.5
-
56
-
-
0035031966
-
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
-
Whelan S, Goldman N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol. 18:691-699.
-
(2001)
Mol Biol Evol.
, vol.18
, pp. 691-699
-
-
Whelan, S.1
Goldman, N.2
-
57
-
-
0035339920
-
Molecular phylogenetics: Stateof-the-art methods for looking into the past
-
Whelan S, Li ó P, Goldman N. 2001. Molecular phylogenetics: stateof-the-art methods for looking into the past. Trends Genet. 17: 262-272.
-
(2001)
Trends Genet.
, vol.17
, pp. 262-272
-
-
Whelan, S.1
Li Ó, P.2
Goldman, N.3
-
58
-
-
84864029746
-
Bringing molecules back into molecular evolution
-
Wilke CO. 2012. Bringing molecules back into molecular evolution. PLoS Comput Biol. 8:e1002572.
-
(2012)
PLoS Comput Biol.
, vol.8
-
-
Wilke, C.O.1
-
59
-
-
0027132974
-
Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
-
Yang Z. 1993. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites.Mol Biol Evol. 10: 1396-1401.
-
(1993)
Mol Biol Evol.
, vol.10
, pp. 1396-1401
-
-
Yang, Z.1
-
60
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591.
-
(2007)
Mol Biol Evol.
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
61
-
-
0031792828
-
Models of amino acid substitution and applications to mitochondrial protein evolution
-
Yang Z, Nielsen R, Masami H. 1998. Models of amino acid substitution and applications to mitochondrial protein evolution.Mol Biol Evol. 15:1600-1611.
-
(1998)
Mol Biol Evol.
, vol.15
, pp. 1600-1611
-
-
Yang, Z.1
Nielsen, R.2
Masami, H.3
|