-
1
-
-
13444302764
-
FunShift: A database of function shift analysis on protein subfamilies
-
Abhiman S, Sonnhammer EL. 2005. FunShift: a database of function shift analysis on protein subfamilies. Nucleic Acids Res. 33:D197-D200.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Abhiman, S.1
Sonnhammer, E.L.2
-
2
-
-
0016355478
-
A new look at the statistical model identification
-
Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Automat Contr. 19:716-723.
-
(1974)
IEEE Trans Automat Contr
, vol.19
, pp. 716-723
-
-
Akaike, H.1
-
4
-
-
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
-
5
-
-
0033954256
-
The protein data bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. 2000. The Protein Data Bank. Nucleic Acids Res. 28:235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
6
-
-
0642340510
-
Amino acid empirical contact energy definitions for fold recognition in the space of contact maps
-
Berrera M, Molinari H, Fogolari F. 2003. Amino acid empirical contact energy definitions for fold recognition in the space of contact maps. BMC Bioinformatics 4:8.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 8
-
-
Berrera, M.1
Molinari, H.2
Fogolari, F.3
-
8
-
-
33748143748
-
Structural determinants of the rate of protein evolution in yeast
-
Bloom JD, Drummond DA, Arnold FH, Wilke CO. 2006. Structural determinants of the rate of protein evolution in yeast. Mol Biol Evol. 23: 1751-1761.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 1751-1761
-
-
Bloom, J.D.1
Drummond, D.A.2
Arnold, F.H.3
Wilke, C.O.4
-
9
-
-
33748781457
-
The dynamic energy landscape of dihydrofolate reductase catalysis
-
Boehr DD, McElheny D, Dyson HJ, Wright PE. 2006. The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313: 1638-1642.
-
(2006)
Science
, vol.313
, pp. 1638-1642
-
-
Boehr, D.D.1
McElheny, D.2
Dyson, H.J.3
Wright, P.E.4
-
10
-
-
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
-
11
-
-
0024733407
-
Intermediates and barrier crossing in a random energy model (with applications to protein folding)
-
Bryngelson JD,Wolynes PG. 1989. Intermediates and barrier crossing in a random energy model (with applications to protein folding). J Phys Chem. 93:6902-6915.
-
(1989)
J Phys Chem
, vol.93
, pp. 6902-6915
-
-
Bryngelson, J.D.1
Wolynes, P.G.2
-
13
-
-
67649795139
-
Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure
-
Burra PV, Zhang Y, Godzik A, Stec B. 2009. Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure. Proc Natl Acad Sci USA. 106:10505-10510.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 10505-10510
-
-
Burra, P.V.1
Zhang, Y.2
Godzik, A.3
Stec, B.4
-
14
-
-
0022706389
-
The relation between the divergence of sequence and structure in proteins
-
Chothia C, Lesk AM. 1986. The relation between the divergence of sequence and structure in proteins. EMBO J. 5:823-826.
-
(1986)
EMBO J
, vol.5
, pp. 823-826
-
-
Chothia, C.1
Lesk, A.M.2
-
15
-
-
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
-
16
-
-
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
-
17
-
-
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
-
18
-
-
0027024416
-
Three-dimensional profiles for analysing protein sequence-structure relationships
-
Eisenberg D, Bowie JU, Luthy R, Choe S. 1992. Three-dimensional profiles for analysing protein sequence-structure relationships. Faraday Discuss. 93:25-34.
-
(1992)
Faraday Discuss
, vol.93
, pp. 25-34
-
-
Eisenberg, D.1
Bowie, J.U.2
Luthy, R.3
Choe, S.4
-
19
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 17:368-376.
-
(1981)
J Mol Evol
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
20
-
-
0000122573
-
PHYLIP-phylogeny inference package (version 3.2)
-
Felsenstein J. 1989. PHYLIP-phylogeny inference package (version 3.2). Cladistics 5:164-166.
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
21
-
-
67650021210
-
Effective knowledge-based potentials
-
Ferrada E, Melo F. 2009. Effective knowledge-based potentials. Protein Sci. 18:1469-1485.
-
(2009)
Protein Sci
, vol.18
, pp. 1469-1485
-
-
Ferrada, E.1
Melo, F.2
-
23
-
-
84892166712
-
Einfluss der Configuration auf die wirkung der Enzyme
-
Fischer E. 1894. Einfluss der Configuration auf die wirkung der Enzyme. Ber Dtsch Chem Ges. 27:2985-2993.
-
(1894)
Ber Dtsch Chem Ges
, vol.27
, pp. 2985-2993
-
-
Fischer, E.1
-
24
-
-
0027943261
-
Conformational isomerism and the diversity of antibodies
-
Foote J, Milstein C. 1994. Conformational isomerism and the diversity of antibodies. Proc Natl Acad Sci USA. 91:10370-10374.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, pp. 10370-10374
-
-
Foote, J.1
Milstein, C.2
-
25
-
-
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
-
26
-
-
33846850375
-
Quaternary structure constraints on evolutionary sequence divergence
-
Fornasari MS, Parisi G, Echave J. 2007. Quaternary structure constraints on evolutionary sequence divergence. Mol Biol Evol. 24:349-351.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 349-351
-
-
Fornasari, M.S.1
Parisi, G.2
Echave, J.3
-
27
-
-
67049155677
-
A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family
-
Friedland GD, Lakomek NA, Griesinger C,Meiler J, Kortemme T. 2009. A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput Biol. 5:e1000393.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Friedland, G.D.1
Lakomek, N.A.2
Griesinger Cmeiler, J.3
Kortemme, T.4
-
28
-
-
33846033844
-
The CATH domain structure database: New protocols and classification levels giveamore comprehensive resource for exploring evolution
-
14 co-authors
-
Greene LH, Lewis TE, Addou S, et al. (14 co-authors). 2007. The CATH domain structure database: new protocols and classification levels giveamore comprehensive resource for exploring evolution. Nucleic Acids Res. 35:D291-D297.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Greene, L.H.1
Lewis, T.E.2
Addou, S.3
-
29
-
-
0023984770
-
Profile scanning for three-dimensional structural patterns in protein sequences
-
Gribskov M, Homyak M, Edenfield J, Eisenberg D. 1988. Profile scanning for three-dimensional structural patterns in protein sequences. Comput Appl Biosci. 4:61-66.
-
(1988)
Comput Appl Biosci
, vol.4
, pp. 61-66
-
-
Gribskov, M.1
Homyak, M.2
Edenfield, J.3
Eisenberg, D.4
-
31
-
-
12344307441
-
Conformational changes observed in enzyme crystal structures upon substrate binding
-
Gutteridge A, Thornton J. 2005. Conformational changes observed in enzyme crystal structures upon substrate binding. J Mol Biol. 346: 21-28.
-
(2005)
J Mol Biol
, vol.346
, pp. 21-28
-
-
Gutteridge, A.1
Thornton, J.2
-
32
-
-
0013817874
-
The influence of amino-acid sequence on protein structure
-
Guzzo AV. 1965. The influence of amino-acid sequence on protein structure. Biophys J. 5:809-822.
-
(1965)
Biophys J.
, vol.5
, pp. 809-822
-
-
Guzzo, A.V.1
-
33
-
-
0034644783
-
Analysis and prediction of functional sub-types from protein sequence alignments
-
Hannenhalli SS, Russell RB. 2000. Analysis and prediction of functional sub-types from protein sequence alignments. J Mol Biol. 303:61-76.
-
(2000)
J Mol Biol
, vol.303
, pp. 61-76
-
-
Hannenhalli, S.S.1
Russell, R.B.2
-
34
-
-
36849048228
-
Intrinsic motions along an enzymatic reaction trajectory
-
12 co-authors
-
Henzler-Wildman KA, Thai V, Lei M, et al. (12 co-authors). 2007. Intrinsic motions along an enzymatic reaction trajectory. Nature 450: 838-844.
-
(2007)
Nature
, vol.450
, pp. 838-844
-
-
Henzler-Wildman, K.A.1
Thai, V.2
Lei, M.3
-
35
-
-
76249122268
-
Biochemistry. An ensemble view of allostery
-
Hilser VJ. 2010. Biochemistry. An ensemble view of allostery. Science 327: 653-654.
-
(2010)
Science
, vol.327
, pp. 653-654
-
-
Hilser, V.J.1
-
36
-
-
0038148710
-
Conformational diversity and protein evolution-A 60-year-old hypothesis revisited
-
James LC, Tawfik DS. 2003. Conformational diversity and protein evolution-a 60-year-old hypothesis revisited. Trends Biochem Sci. 28: 361-368.
-
(2003)
Trends Biochem Sci
, vol.28
, pp. 361-368
-
-
James, L.C.1
Tawfik, D.S.2
-
37
-
-
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
-
38
-
-
78651327630
-
PCDB: A database of proteins with conformational diversity
-
Juritz J, Fernandez-Alberti S, Parisi G. 2011. PCDB: a database of proteins with conformational diversity. Nucleic Acids Res. 39(1 suppl): D475-D479.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.1 SUPPL.
-
-
Juritz, J.1
Fernandez-Alberti, S.2
Parisi, G.3
-
39
-
-
0025058563
-
Escherichia coli aspartate transcarbamoylase: The molecular basis for a concerted allosteric transition
-
Kantrowitz ER, Lipscomb WN. 1990. Escherichia coli aspartate transcarbamoylase: the molecular basis for a concerted allosteric transition. Trends Biochem Sci. 15:53-59.
-
(1990)
Trends Biochem Sci
, vol.15
, pp. 53-59
-
-
Kantrowitz, E.R.1
Lipscomb, W.N.2
-
40
-
-
0031301752
-
Predicting protein structure using hidden Markov models
-
Karplus K, Sjolander K, Barrett C, Cline M, Haussler D, Hughey R, Holm L, Sander C. 1997. Predicting protein structure using hidden Markov models. Proteins (Suppl 1), 134-139.
-
(1997)
Proteins
, Issue.SUPPL. 1
, pp. 134-139
-
-
Karplus, K.1
Sjolander, K.2
Barrett, C.3
Cline, M.4
Haussler, D.5
Hughey, R.6
Holm, L.7
Sander, C.8
-
41
-
-
18744371588
-
Molecular dynamics and protein function
-
Karplus M, Kuriyan J. 2005. Molecular dynamics and protein function. Proc Natl Acad Sci USA. 102:6679-6685.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 6679-6685
-
-
Karplus, M.1
Kuriyan, J.2
-
42
-
-
0001443732
-
Heterogeneity of the binding sites of bovine serum albumin
-
Karush F. 1950. Heterogeneity of the binding sites of bovine serum albumin. J Am Chem Soc. 72:2705-2713.
-
(1950)
J Am Chem Soc
, vol.72
, pp. 2705-2713
-
-
Karush, F.1
-
43
-
-
0034029144
-
Proteins with similar architecture exhibit similar large-scale dynamic behavior
-
Keskin O, Jernigan RL, Bahar I. 2000. Proteins with similar architecture exhibit similar large-scale dynamic behavior. Biophys J. 78:2093-2106.
-
(2000)
Biophys J
, vol.78
, pp. 2093-2106
-
-
Keskin, O.1
Jernigan, R.L.2
Bahar, I.3
-
44
-
-
77953771357
-
Statistical potentials for improved structurally constrained evolutionary models
-
Kleinman CL, Rodrigue N, Lartillot N, Philippe H. 2010. Statistical potentials for improved structurally constrained evolutionary models. Mol Biol Evol. 27:1546-1560.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 1546-1560
-
-
Kleinman, C.L.1
Rodrigue, N.2
Lartillot, N.3
Philippe, H.4
-
45
-
-
37849031192
-
Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments
-
Kondrashov DA, Zhang W, Aranda R, Stec B, Phillips GN Jr. 2008. Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments. Proteins 70: 353-362.
-
(2008)
Proteins
, vol.70
, pp. 353-362
-
-
Kondrashov, D.A.1
Zhang, W.2
Aranda, R.3
Stec, B.4
Phillips Jr., G.N.5
-
46
-
-
0028808763
-
Context-dependent optimal substitution matrices
-
Koshi JM, Goldstein RA. 1995. Context-dependent optimal substitution matrices. Protein Eng. 8:641-645.
-
(1995)
Protein Eng
, vol.8
, pp. 641-645
-
-
Koshi, J.M.1
Goldstein, R.A.2
-
48
-
-
0028181441
-
Hidden Markov models in computational biology. Applications to protein modeling
-
Krogh A, Brown M, Mian IS, Sjolander K, Haussler D. 1994. Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol. 235:1501-1531.
-
(1994)
J Mol Biol
, vol.235
, pp. 1501-1531
-
-
Krogh, A.1
Brown, M.2
Mian, I.S.3
Sjolander, K.4
Haussler, D.5
-
49
-
-
0033970020
-
Folding and binding cascades: Dynamic landscapes and population shifts
-
Kumar S, Ma B, Tsai CJ, Sinha N, Nussinov R. 2000. Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci. 9: 10-19.
-
(2000)
Protein Sci
, vol.9
, pp. 10-19
-
-
Kumar, S.1
Ma, B.2
Tsai, C.J.3
Sinha, N.4
Nussinov, R.5
-
50
-
-
45849131354
-
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution
-
Lange OF, Lakomek NA, Fares C, Schroder GF, Walter KF, Becker S, Meiler J, Grubmuller H, Griesinger C, de Groot BL. 2008. Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science 320:1471-1475.
-
(2008)
Science
, vol.320
, pp. 1471-1475
-
-
Lange, O.F.1
Lakomek, N.A.2
Fares, C.3
Schroder, G.F.4
Walter, K.F.5
Becker, S.6
Meiler, J.7
Grubmuller, H.8
Griesinger, C.9
De Groot, B.L.10
-
51
-
-
45849154166
-
An improved general amino acid replacement matrix
-
Le SQ, Gascuel O. 2008. An improved general amino acid replacement matrix. Mol Biol Evol. 25:1307-1320.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 1307-1320
-
-
Le, S.Q.1
Gascuel, O.2
-
52
-
-
0019332167
-
How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins
-
Lesk AM, Chothia C. 1980. How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J Mol Biol. 136:225-270.
-
(1980)
J Mol Biol
, vol.136
, pp. 225-270
-
-
Lesk, A.M.1
Chothia, C.2
-
53
-
-
0018093765
-
Conformational preferences of amino acids in globular proteins
-
Levitt M. 1978. Conformational preferences of amino acids in globular proteins. Biochemistry 17:4277-4285.
-
(1978)
Biochemistry
, vol.17
, pp. 4277-4285
-
-
Levitt, M.1
-
54
-
-
0026610767
-
Assessment of protein models with three-dimensional profiles
-
Luthy R, Bowie JU, Eisenberg D. 1992. Assessment of protein models with three-dimensional profiles. Nature 356:83-85.
-
(1992)
Nature
, vol.356
, pp. 83-85
-
-
Luthy, R.1
Bowie, J.U.2
Eisenberg, D.3
-
55
-
-
0025997601
-
Secondary structure-based profiles: Use of structure-conserving scoring tables in searching protein sequence databases for structural similarities
-
Luthy R, McLachlan AD, Eisenberg D. 1991. Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities. Proteins 10: 229-239.
-
(1991)
Proteins
, vol.10
, pp. 229-239
-
-
Luthy, R.1
McLachlan, A.D.2
Eisenberg, D.3
-
56
-
-
0036147568
-
Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations
-
Ma B, Shatsky M,Wolfson HJ, Nussinov R. 2002. Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci. 11:184-197.
-
(2002)
Protein Sci
, vol.11
, pp. 184-197
-
-
Ma, B.1
Shatsky Mwolfson, H.J.2
Nussinov, R.3
-
57
-
-
49049096095
-
Evolutionary conservation of protein vibrational dynamics
-
Maguid S, Fernandez-Alberti S, Echave J. 2008. Evolutionary conservation of protein vibrational dynamics. Gene 422:7-13.
-
(2008)
Gene
, vol.422
, pp. 7-13
-
-
Maguid, S.1
Fernandez-Alberti, S.2
Echave, J.3
-
58
-
-
23244450294
-
Exploring the common dynamics of homologous proteins. Application to the globin family
-
Maguid S, Fernandez-Alberti S, Ferrelli L, Echave J. 2005. Exploring the common dynamics of homologous proteins. Application to the globin family. Biophys J. 89:3-13.
-
(2005)
Biophys J
, vol.89
, pp. 3-13
-
-
Maguid, S.1
Fernandez-Alberti, S.2
Ferrelli, L.3
Echave, J.4
-
60
-
-
78651189765
-
On the nature of allosteric transitions: A plausible model
-
Monod J, Wyman J, Changeux JP. 1965. On the nature of allosteric transitions: a plausible model. J Mol Biol. 12:88-118.
-
(1965)
J Mol Biol
, vol.12
, pp. 88-118
-
-
Monod, J.1
Wyman, J.2
Changeux, J.P.3
-
61
-
-
34547631623
-
Prevention of amyloid-like aggregation as a driving force of protein evolution
-
Monsellier E, Chiti F. 2007. Prevention of amyloid-like aggregation as a driving force of protein evolution. EMBO Rep. 8:737-742.
-
(2007)
EMBO Rep
, vol.8
, pp. 737-742
-
-
Monsellier, E.1
Chiti, F.2
-
63
-
-
0036839162
-
MAMMOTH (matching molecular models obtained from theory): An automated method for model comparison
-
Ortiz AR, Strauss CE, Olmea O. 2002. MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci. 11:2606-2621.
-
(2002)
Protein Sci
, vol.11
, pp. 2606-2621
-
-
Ortiz, A.R.1
Strauss, C.E.2
Olmea, O.3
-
64
-
-
0026474167
-
Structural constraints on residue substitution
-
Overington J. 1992. Structural constraints on residue substitution. Genet Eng (N Y). 14:231-249.
-
(1992)
Genet Eng (N y
, vol.14
, pp. 231-249
-
-
Overington, J.1
-
65
-
-
0025104478
-
Tertiary structural constraints on protein evolutionary diversity: Templates, key residues and structure prediction
-
Overington J, Johnson MS, Sali A, Blundell TL. 1990. Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proc R Soc B Biol Sci. 241: 132-145.
-
(1990)
Proc R Soc B Biol Sci
, vol.241
, pp. 132-145
-
-
Overington, J.1
Johnson, M.S.2
Sali, A.3
Blundell, T.L.4
-
66
-
-
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
-
67
-
-
33845548778
-
The structurally constrained protein evolution model accounts for sequence patterns of the LbetaH superfamily
-
Parisi G, Echave J. 2004. The structurally constrained protein evolution model accounts for sequence patterns of the LbetaH superfamily. BMC Evol Biol. 4:41.
-
(2004)
BMC Evol Biol
, vol.4
, pp. 41
-
-
Parisi, G.1
Echave, J.2
-
68
-
-
13444305208
-
Generality of the structurally constrained protein evolution model: Assessment on representatives of the four main fold classes
-
Parisi G, Echave J. 2005. Generality of the structurally constrained protein evolution model: assessment on representatives of the four main fold classes. Gene 345:45-53.
-
(2005)
Gene
, vol.345
, pp. 45-53
-
-
Parisi, G.1
Echave, J.2
-
69
-
-
15844406550
-
HyPhy: Hypothesis testing using phylogenies
-
Pond SL, Frost SD, Muse SV. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21:676-679.
-
(2005)
Bioinformatics
, vol.21
, pp. 676-679
-
-
Pond, S.L.1
Frost, S.D.2
Muse, S.V.3
-
70
-
-
0027288463
-
The HSSP database of protein structuresequence alignments
-
Sander C, Schneider R. 1993. The HSSP database of protein structuresequence alignments. Nucleic Acids Res. 21:3105-3109.
-
(1993)
Nucleic Acids Res
, vol.21
, pp. 3105-3109
-
-
Sander, C.1
Schneider, R.2
-
72
-
-
0035853126
-
Point mutations and sequence variability in proteins: Redistributions of preexisting populations
-
Sinha N, Nussinov R. 2001. Point mutations and sequence variability in proteins: redistributions of preexisting populations. Proc Natl Acad Sci USA. 98:3139-3144.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 3139-3144
-
-
Sinha, N.1
Nussinov, R.2
-
73
-
-
64849101493
-
Protein dynamism and evolvability
-
Tokuriki N, Tawfik DS. 2009. Protein dynamism and evolvability. Science 324:203-207.
-
(2009)
Science
, vol.324
, pp. 203-207
-
-
Tokuriki, N.1
Tawfik, D.S.2
-
74
-
-
0033056708
-
Folding funnels, binding funnels, and protein function
-
Tsai CJ, Kumar S, Ma B, Nussinov R. 1999. Folding funnels, binding funnels, and protein function. Protein Sci. 8:1181-1190.
-
(1999)
Protein Sci
, vol.8
, pp. 1181-1190
-
-
Tsai, C.J.1
Kumar, S.2
Ma, B.3
Nussinov, R.4
-
75
-
-
0033621104
-
Folding and binding cascades: Shifts in energy landscapes
-
Tsai CJ, Ma B, Nussinov R. 1999. Folding and binding cascades: shifts in energy landscapes. Proc Natl Acad Sci USA. 96:9970-9972.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 9970-9972
-
-
Tsai, C.J.1
Ma, B.2
Nussinov, R.3
-
76
-
-
34547399613
-
A solution NMR study showing that active site ligands and nucleotides directly perturb the allosteric equilibriumin aspartate transcarbamoylase
-
Velyvis A, Yang YR, Schachman HK, Kay LE. 2007. A solution NMR study showing that active site ligands and nucleotides directly perturb the allosteric equilibriumin aspartate transcarbamoylase. Proc Natl Acad Sci USA. 104:8815-8820.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 8815-8820
-
-
Velyvis, A.1
Yang, Y.R.2
Schachman, H.K.3
Kay, L.E.4
-
77
-
-
0035937443
-
Two-state allosteric behavior in a single-domain signaling protein
-
Volkman BF, Lipson D, Wemmer DE, Kern D. 2001. Two-state allosteric behavior in a single-domain signaling protein. Science 291: 2429-2433.
-
(2001)
Science
, vol.291
, pp. 2429-2433
-
-
Volkman, B.F.1
Lipson, D.2
Wemmer, D.E.3
Kern, D.4
-
78
-
-
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
-
79
-
-
77958476428
-
Relative contributions of intrinsic structural-functional constraints and translation rate to the evolution of protein-coding genes
-
Wolf YI, Gopich IV, Lipman DJ, Koonin EV. 2010. Relative contributions of intrinsic structural-functional constraints and translation rate to the evolution of protein-coding genes. Genome Biol Evol. 2:190-199.
-
(2010)
Genome Biol Evol
, vol.2
, pp. 190-199
-
-
Wolf, Y.I.1
Gopich, I.V.2
Lipman, D.J.3
Koonin, E.V.4
-
80
-
-
79951681020
-
Protein functional landscapes, dynamics, allostery: A tortuous path towards a universal theoretical framework
-
Zhuravlev PI, Papoian GA. 2010. Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework. Q Rev Biophys. 43:295-332.
-
(2010)
Q Rev Biophys
, vol.43
, pp. 295-332
-
-
Zhuravlev, P.I.1
Papoian, G.A.2
-
81
-
-
0036298514
-
Relation between sequence and structure of HIV-1 protease inhibitor complexes: A model system for the analysis of protein flexibility
-
Zoete V, Michielin O, Karplus M. 2002. Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility. J Mol Biol. 315:21-52.
-
(2002)
J Mol Biol
, vol.315
, pp. 21-52
-
-
Zoete, V.1
Michielin, O.2
Karplus, M.3
|