-
1
-
-
0033969946
-
Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica
-
Bustamante CD, Townsend JP, Hartl DL. 2000. Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica. Molecular Biology and Evolution 17(2):301-308 DOI 10.1093/oxfordjournals.molbev.a026310.
-
(2000)
Molecular Biology and Evolution
, vol.17
, Issue.2
, pp. 301-308
-
-
Bustamante, C.D.1
Townsend, J.P.2
Hartl, D.L.3
-
2
-
-
65349140199
-
Solvent exposure imparts similar selective pressures across a range of yeast proteins
-
Conant GC, Stadler PF. 2009. Solvent exposure imparts similar selective pressures across a range of yeast proteins. Molecular Biology and Evolution 26(5):1155-1161 DOI 10.1093/molbev/msp031.
-
(2009)
Molecular Biology and Evolution
, vol.26
, Issue.5
, pp. 1155-1161
-
-
Conant, G.C.1
Stadler, P.F.2
-
3
-
-
43549093267
-
Evolutionary divergence of protein structure: the linearly forced elastic network model
-
Echave J. 2008. Evolutionary divergence of protein structure: the linearly forced elastic network model. Chemical Physics Letters 457(4-6):413-416 DOI 10.1016/j.cplett.2008.04.042.
-
(2008)
Chemical Physics Letters
, vol.457
, Issue.4-6
, pp. 413-416
-
-
Echave, J.1
-
4
-
-
77949400204
-
A perturbative view of protein structural variation
-
Echave J, Ferńandez FM. 2010. A perturbative view of protein structural variation. Proteins 78(1):173-180 DOI 10.1002/prot.22553.
-
(2010)
Proteins
, vol.78
, Issue.1
, pp. 173-180
-
-
Echave, J.1
Ferńandez, F.M.2
-
5
-
-
84928811331
-
Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites
-
Echave J, Jackson EL, Wilke CO. 2015. Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites. Physical Biology 12:025002 DOI 10.1088/1478-3975/12/2/025002.
-
(2015)
Physical Biology
, vol.12
-
-
Echave, J.1
Jackson, E.L.2
Wilke, C.O.3
-
6
-
-
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. Molecular Biology and Evolution 26:2387-2395 DOI 10.1093/molbev/msp146.
-
(2009)
Molecular Biology and Evolution
, vol.26
, pp. 2387-2395
-
-
Franzosa, E.A.1
Xia, Y.2
-
7
-
-
84899480289
-
A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility
-
Huang T-T, Marcos ML, Hwang J-K, 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 Evolutionary Biology 14:78 DOI 10.1186/1471-2148-14-78.
-
(2014)
BMC Evolutionary Biology
, vol.14
, pp. 78
-
-
Huang, T.-T.1
Marcos, M.L.2
Hwang, J.-K.3
Echave, J.4
-
8
-
-
13744252890
-
MAFFT version 5: improvement in accuracy of multiple sequence alignment
-
Katoh K, Kuma K-I, Toh H, Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research 33:511-518 DOI 10.1093/nar/gki198.
-
(2005)
Nucleic Acids Research
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.-I.2
Toh, H.3
Miyata, T.4
-
9
-
-
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. Molecular Biology and Evolution 30:772-780 DOI 10.1093/molbev/mst010.
-
(2013)
Molecular Biology and Evolution
, vol.30
, pp. 772-780
-
-
Katoh, K.1
Standley, D.M.2
-
10
-
-
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 APJ, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjolander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S. 2012. The interface of protein structure, protein biophysics, and molecular evolution. Protein Science 21(6):769-785 DOI 10.1002/pro.2071.
-
(2012)
Protein Science
, vol.21
, Issue.6
, 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.J.8
Dokholyan, N.V.9
Echave, J.10
Elofsson, A.11
Gerloff, D.L.12
Goldstein, R.A.13
Grahnen, J.A.14
Holder, M.T.15
Lakner, C.16
Lartillot, N.17
Lovell, S.C.18
Naylor, G.19
Perica, T.20
Pollock, D.D.21
Pupko, T.22
Regan, L.23
Roger, A.24
Rubinstein, N.25
Shakhnovich, E.26
Sjolander, K.27
Sunyaev, S.28
Teufel, A.I.29
Thorne, J.L.30
Thornton, J.W.31
Weinreich, D.M.32
Whelan, S.33
more..
-
11
-
-
47349097554
-
Deriving protein dynamical properties from weighted protein contact number
-
Lin CP, Huang SW, Lai YL, Yen SC, Shih CH, Lu CH, Huang CC, Hwang JK. 2008. Deriving protein dynamical properties from weighted protein contact number. Proteins 72:929-935 DOI 10.1002/prot.21983.
-
(2008)
Proteins
, vol.72
, pp. 929-935
-
-
Lin, C.P.1
Huang, S.W.2
Lai, Y.L.3
Yen, S.C.4
Shih, C.H.5
Lu, C.H.6
Huang, C.C.7
Hwang, J.K.8
-
12
-
-
4143051195
-
Comparison of site-specific rate-inference methods: Bayesian methods are superior
-
Mayrose I, Graur D, Ben-Tal N, Pupko T. 2004. Comparison of site-specific rate-inference methods: Bayesian methods are superior. Molecular Biology and Evolution 21:1781-1791 DOI 10.1093/molbev/msh194.
-
(2004)
Molecular Biology and Evolution
, vol.21
, pp. 1781-1791
-
-
Mayrose, I.1
Graur, D.2
Ben-Tal, N.3
Pupko, T.4
-
13
-
-
79958187925
-
The relationship between relative solvent accessibility and evolutionary rate in protein evolution
-
Ramsey DC, Scherrer MP, Zhou T, Wilke CO. 2011. The relationship between relative solvent accessibility and evolutionary rate in protein evolution. Genetics 188(2):479-488 DOI 10.1534/genetics.111.128025.
-
(2011)
Genetics
, vol.188
, Issue.2
, pp. 479-488
-
-
Ramsey, D.C.1
Scherrer, M.P.2
Zhou, T.3
Wilke, C.O.4
-
14
-
-
84963641621
-
R: a language and environment for statistical computing
-
Vienna: R Foundation for Statistical Computing
-
R Core Team. 2014. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing.
-
(2014)
-
-
-
15
-
-
84919760834
-
Predicting evolutionary site variability from structure in viral proteins: buriedness, packing, flexibility, and design
-
Shahmoradi A, Sydykova DK, Spielman SJ, Jackson EL, Dawson ET, Meyer AG, Wilke CO. 2014. Predicting evolutionary site variability from structure in viral proteins: buriedness, packing, flexibility, and design. Journal of Molecular Evolution 79(3-4):130-142 DOI 10.1007/s00239-014-9644-x.
-
(2014)
Journal of Molecular Evolution
, vol.79
, Issue.3-4
, pp. 130-142
-
-
Shahmoradi, A.1
Sydykova, D.K.2
Spielman, S.J.3
Jackson, E.L.4
Dawson, E.T.5
Meyer, A.G.6
Wilke, C.O.7
-
16
-
-
84862785625
-
Evolutionary information hidden in a single protein structure
-
Shih C-H, Hwang J-K. 2012. Evolutionary information hidden in a single protein structure. Proteins 80(6):1647-1657 DOI 10.1002/prot.24058.
-
(2012)
Proteins
, vol.80
, Issue.6
, pp. 1647-1657
-
-
Shih, C.-H.1
Hwang, J.-K.2
-
17
-
-
84908154345
-
Biophysics of protein evolution and evolutionary protein biophysics
-
Sikosek T, Chan HS. 2014. Biophysics of protein evolution and evolutionary protein biophysics. Journal of the Royal Society, Interface / the Royal Society 11(100):20140419-20140419 DOI 10.1098/rsif.2014.0419.
-
(2014)
Journal of the Royal Society, Interface / the Royal Society
, vol.11
, Issue.100
, pp. 20140419-20140419
-
-
Sikosek, T.1
Chan, H.S.2
-
18
-
-
84899553363
-
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
-
Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312-1313 DOI 10.1093/bioinformatics/btu033.
-
(2014)
Bioinformatics
, vol.30
, pp. 1312-1313
-
-
Stamatakis, A.1
-
19
-
-
84888331478
-
Maximum allowed solvent accessibilites of residues in proteins
-
Tien MZ, Meyer AG, Sydykova DK, Spielman SJ, Wilke CO. 2013. Maximum allowed solvent accessibilites of residues in proteins. PLoS ONE 8(11):e80635 DOI 10.1371/journal.pone.0080635.
-
(2013)
PLoS ONE
, vol.8
, Issue.11
-
-
Tien, M.Z.1
Meyer, A.G.2
Sydykova, D.K.3
Spielman, S.J.4
Wilke, C.O.5
-
21
-
-
84904630632
-
Local packing density is the main structural determinant of the rate of protein sequence evolution at site level
-
Yeh SW, Huang TT, Liu JW, Yu SH, Shih CH, Hwang JK, Echave J. 2014a. Local packing density is the main structural determinant of the rate of protein sequence evolution at site level. BioMed Research International 2014:572409 DOI 10.1155/2014/572409.
-
(2014)
BioMed Research International
, vol.2014
-
-
Yeh, S.W.1
Huang, T.T.2
Liu, J.W.3
Yu, S.H.4
Shih, C.H.5
Hwang, J.K.6
Echave, J.7
-
22
-
-
84891761205
-
Site-specific structural constraints on protein sequence evolutionary divergence: local packing density versus solvent exposure
-
Yeh SW, Liu JW, Yu SH, Shih CH, Hwang JK, Echave J. 2014b. Site-specific structural constraints on protein sequence evolutionary divergence: local packing density versus solvent exposure. Molecular Biology and Evolution 31:135-139 DOI 10.1093/molbev/mst178.
-
(2014)
Molecular Biology and Evolution
, vol.31
, pp. 135-139
-
-
Yeh, S.W.1
Liu, J.W.2
Yu, S.H.3
Shih, C.H.4
Hwang, J.K.5
Echave, J.6
|