-
1
-
-
33646943202
-
Molecular dynamics: survey of methods for simulating the activity of proteins
-
Adcock S.A., and McCammon J.A. Molecular dynamics: survey of methods for simulating the activity of proteins. Chem. Rev. 106 (2006) 1589-1615
-
(2006)
Chem. Rev.
, vol.106
, pp. 1589-1615
-
-
Adcock, S.A.1
McCammon, J.A.2
-
2
-
-
17044458224
-
Mapping the paratope of anti-cd4 recombinant fab 13b8.2 by combining parallel peptide synthesis and site-directed mutagenesis
-
Báes C., Briant-Longuet L., Cerutti M., Heitz F., Troadec S., Pugniáere M., Roquet F., Molina F., Casset F., Bresson D., et al. Mapping the paratope of anti-cd4 recombinant fab 13b8.2 by combining parallel peptide synthesis and site-directed mutagenesis. J. Biol. Chem. 278 (2003) 14265-14273
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 14265-14273
-
-
Báes, C.1
Briant-Longuet, L.2
Cerutti, M.3
Heitz, F.4
Troadec, S.5
Pugniáere, M.6
Roquet, F.7
Molina, F.8
Casset, F.9
Bresson, D.10
-
3
-
-
8344256552
-
Recombinant protein folding and misfolding in Escherichia coli
-
Baneyx F., and Mujacic M. Recombinant protein folding and misfolding in Escherichia coli. Nat. Biotechnol. 22 (2004) 1399-1408
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 1399-1408
-
-
Baneyx, F.1
Mujacic, M.2
-
4
-
-
4544386044
-
Carbopeptoid folding: effects of stereochemistry, chain length, and solvent
-
Baron R., Bakowies D., and van Gunsteren W.F. Carbopeptoid folding: effects of stereochemistry, chain length, and solvent. Angew. Chem. Int. Ed. 43 (2004) 4055-4059
-
(2004)
Angew. Chem. Int. Ed.
, vol.43
, pp. 4055-4059
-
-
Baron, R.1
Bakowies, D.2
van Gunsteren, W.F.3
-
5
-
-
34548667196
-
Dynamics, hydration, and motional averaging of a loop-gated artificial protein cavity: the w191g mutant of cytochrome c peroxidase in water as revealed by molecular dynamics simulations
-
Baron R., and McCammon J.A. Dynamics, hydration, and motional averaging of a loop-gated artificial protein cavity: the w191g mutant of cytochrome c peroxidase in water as revealed by molecular dynamics simulations. Biochemistry 46 (2007) 10629-10642
-
(2007)
Biochemistry
, vol.46
, pp. 10629-10642
-
-
Baron, R.1
McCammon, J.A.2
-
6
-
-
58149149594
-
E9-im9 colicin dnase-immunity protein biomolecular association in water: a multiple-copy and accelerated molecular dynamics simulation study
-
Baron R., Wong S.E., de Oliveira C.A., and McCammon J.A. E9-im9 colicin dnase-immunity protein biomolecular association in water: a multiple-copy and accelerated molecular dynamics simulation study. J. Phys. Chem. B 112 (2008) 16802-16814
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 16802-16814
-
-
Baron, R.1
Wong, S.E.2
de Oliveira, C.A.3
McCammon, J.A.4
-
7
-
-
33750587438
-
Molecular-dynamics with coupling to an external bath
-
Berendsen H.J.C., Postma J.P.M., Vangunsteren W.F., Dinola A., and Haak J.R. Molecular-dynamics with coupling to an external bath. J. Chem. Phys. 81 (1984) 3684-3690
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Vangunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
8
-
-
27144511241
-
Engineering novel binding proteins from non-immunoglobulin domains
-
Binz H.K., Amstutz P., and Plueckthun A. Engineering novel binding proteins from non-immunoglobulin domains. Nat. Biotechnol. 23 (2005) 1257-1268
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 1257-1268
-
-
Binz, H.K.1
Amstutz, P.2
Plueckthun, A.3
-
9
-
-
23644452792
-
Engineered proteins as specific binding reagents
-
Binz H.K., and Plueckthun A. Engineered proteins as specific binding reagents. Curr. Opin. Biotechnol. 16 (2005) 459-469
-
(2005)
Curr. Opin. Biotechnol.
, vol.16
, pp. 459-469
-
-
Binz, H.K.1
Plueckthun, A.2
-
10
-
-
59449092142
-
Molecular dynamics simulation of the acidic compact state of apomyoglobin from yellowfin tuna
-
Bismuto E., Di Maggio E., Pleus S., Sikor M., Rocker C., Nienhaus G.U., and Lamb D.C. Molecular dynamics simulation of the acidic compact state of apomyoglobin from yellowfin tuna. Proteins: Struct. Funct. Bioinformatics 74 (2009) 273-290
-
(2009)
Proteins: Struct. Funct. Bioinformatics
, vol.74
, pp. 273-290
-
-
Bismuto, E.1
Di Maggio, E.2
Pleus, S.3
Sikor, M.4
Rocker, C.5
Nienhaus, G.U.6
Lamb, D.C.7
-
11
-
-
65349192961
-
Engineering an ultra-stable affinity reagent based on top7
-
Boschek C.B., Apiyo D.O., Soares T.A., Engelmann H.E., Pefaur N.B., Straatsma T.P., and Baird C.L. Engineering an ultra-stable affinity reagent based on top7. Protein Eng. Des. Sel. 22 (2009) 325-332
-
(2009)
Protein Eng. Des. Sel.
, vol.22
, pp. 325-332
-
-
Boschek, C.B.1
Apiyo, D.O.2
Soares, T.A.3
Engelmann, H.E.4
Pefaur, N.B.5
Straatsma, T.P.6
Baird, C.L.7
-
12
-
-
0029011701
-
A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules
-
Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., and Kollman P.A. A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules. J. Am. Chem. Soc. 117 (1995) 5179-5197
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
13
-
-
0037193986
-
Molecular basis of cold adaptation
-
D'Amico S., Claverie P., Collins T., Georlette D., Gratia E., Hoyoux A., Meuwis M.A., Feller G., and Gerday C. Molecular basis of cold adaptation. Philos. Trans. R. Soc. Lond. B Biol. Sci. 357 (2002) 917-925
-
(2002)
Philos. Trans. R. Soc. Lond. B Biol. Sci.
, vol.357
, pp. 917-925
-
-
D'Amico, S.1
Claverie, P.2
Collins, T.3
Georlette, D.4
Gratia, E.5
Hoyoux, A.6
Meuwis, M.A.7
Feller, G.8
Gerday, C.9
-
14
-
-
33645498972
-
Psychrophilic microorganisms: challenges for life
-
D'Amico S., Collins T., Marx J.C., Feller G., and Gerday C. Psychrophilic microorganisms: challenges for life. EMBO Rep. 7 (2006) 385-389
-
(2006)
EMBO Rep.
, vol.7
, pp. 385-389
-
-
D'Amico, S.1
Collins, T.2
Marx, J.C.3
Feller, G.4
Gerday, C.5
-
15
-
-
0037195912
-
Dual effects of an extra disulfide bond on the activity and stability of a cold-adapted alpha-amylase
-
D'Amico S., Gerday C., and Feller G. Dual effects of an extra disulfide bond on the activity and stability of a cold-adapted alpha-amylase. J. Biol. Chem. 277 (2002) 46110-46115
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 46110-46115
-
-
D'Amico, S.1
Gerday, C.2
Feller, G.3
-
16
-
-
0035854688
-
Structural determinants of cold adaptation and stability in a large protein
-
D'Amico S., Gerday C., and Feller G. Structural determinants of cold adaptation and stability in a large protein. J. Biol. Chem. 276 (2001) 25791-25796
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 25791-25796
-
-
D'Amico, S.1
Gerday, C.2
Feller, G.3
-
17
-
-
0041384407
-
Temperature adaptation of proteins: engineering mesophilic-like activity and stability in a cold-adapted alpha-amylase
-
D'Amico S., Gerday C., and Feller G. Temperature adaptation of proteins: engineering mesophilic-like activity and stability in a cold-adapted alpha-amylase. J. Mol. Biol. 332 (2003) 981-988
-
(2003)
J. Mol. Biol.
, vol.332
, pp. 981-988
-
-
D'Amico, S.1
Gerday, C.2
Feller, G.3
-
18
-
-
0037424370
-
Activity-stability relationships in extremophilic enzymes
-
D'Amico S., Marx J.C., Gerday C., and Feller G. Activity-stability relationships in extremophilic enzymes. J. Biol. Chem. 278 (2003) 7891-7896
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 7891-7896
-
-
D'Amico, S.1
Marx, J.C.2
Gerday, C.3
Feller, G.4
-
19
-
-
34548741301
-
A tetrapeptide fragment-based design method results in highly stable artificial proteins
-
Dalluege R., Oschmann J., Birkenmeier O., Luecke C., Lilie H., Rudolph R., and Lange C. A tetrapeptide fragment-based design method results in highly stable artificial proteins. Proteins: Struct. Funct. Bioinformatics 68 (2007) 839-849
-
(2007)
Proteins: Struct. Funct. Bioinformatics
, vol.68
, pp. 839-849
-
-
Dalluege, R.1
Oschmann, J.2
Birkenmeier, O.3
Luecke, C.4
Lilie, H.5
Rudolph, R.6
Lange, C.7
-
20
-
-
33645961739
-
A smooth particle mesh ewald method
-
Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H., and Pedersen L.G. A smooth particle mesh ewald method. J. Chem. Phys. 103 (1995) 8577-8593
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
21
-
-
18744382161
-
Comparative study of generalized born models: protein dynamics
-
Fan H., Mark A.E., Zhu J., and Honig B. Comparative study of generalized born models: protein dynamics. Proc. Natl. Acad. Sci. U.S.A. 102 (2005) 6760-6764
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 6760-6764
-
-
Fan, H.1
Mark, A.E.2
Zhu, J.3
Honig, B.4
-
22
-
-
0032524655
-
Characterization of the c-terminal propeptide involved in bacterial wall spanning of alpha-amylase from the psychrophile alteromonas haloplanctis
-
Feller G., D'Amico S., Benotmane A.M., Joly F., Van Beeumen J., and Gerday C. Characterization of the c-terminal propeptide involved in bacterial wall spanning of alpha-amylase from the psychrophile alteromonas haloplanctis. J. Biol. Chem. 273 (1998) 12109-12115
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 12109-12115
-
-
Feller, G.1
D'Amico, S.2
Benotmane, A.M.3
Joly, F.4
Van Beeumen, J.5
Gerday, C.6
-
23
-
-
33644536727
-
Genetic selection for protein solubility enabled by the folding quality control feature of the twin-arginine translocation pathway
-
Fisher A.C., Kim W., and DeLisa M.P. Genetic selection for protein solubility enabled by the folding quality control feature of the twin-arginine translocation pathway. Protein Sci. 15 (2006) 449-458
-
(2006)
Protein Sci.
, vol.15
, pp. 449-458
-
-
Fisher, A.C.1
Kim, W.2
DeLisa, M.P.3
-
24
-
-
0030037332
-
The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: how well is the X-ray structure "maintained"?
-
Fox T., and Kollman P.A. The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: how well is the X-ray structure "maintained"?. Proteins: Struct. Funct. Bioinformatics 25 (1996) 315-334
-
(1996)
Proteins: Struct. Funct. Bioinformatics
, vol.25
, pp. 315-334
-
-
Fox, T.1
Kollman, P.A.2
-
25
-
-
34347380371
-
Phage display selection of affibody molecules with specific binding to the extracellular domain of the epidermal growth factor receptor
-
Friedman M., Nordberg E., Hoiden-Guthenberg I., Brisimar H., Adams G.P., Nilsson F.Y., Carlss J., and Stahl S. Phage display selection of affibody molecules with specific binding to the extracellular domain of the epidermal growth factor receptor. Protein Eng. Des. Sel. 20 (2007) 189-199
-
(2007)
Protein Eng. Des. Sel.
, vol.20
, pp. 189-199
-
-
Friedman, M.1
Nordberg, E.2
Hoiden-Guthenberg, I.3
Brisimar, H.4
Adams, G.P.5
Nilsson, F.Y.6
Carlss, J.7
Stahl, S.8
-
26
-
-
67649872364
-
Engineered protein scaffolds as next-generation antibody therapeutics
-
Gebauer M., and Skerra A. Engineered protein scaffolds as next-generation antibody therapeutics. Curr. Opin. Chem. Biol. 13 (2009) 245-255
-
(2009)
Curr. Opin. Chem. Biol.
, vol.13
, pp. 245-255
-
-
Gebauer, M.1
Skerra, A.2
-
27
-
-
0029989229
-
Expression of correctly folded proteins in Escherichia coli
-
Georgiou G., and Valax P. Expression of correctly folded proteins in Escherichia coli. Curr. Opin. Biotechnol. 7 (1996) 190-197
-
(1996)
Curr. Opin. Biotechnol.
, vol.7
, pp. 190-197
-
-
Georgiou, G.1
Valax, P.2
-
28
-
-
10744230827
-
Some like it cold: biocatalysis at low temperatures
-
Georlette D., Blaise V., Collins T., D'Amico S., Gratia E., Hoyoux A., Marx J.C., Sonan G., Feller G., and Gerday C. Some like it cold: biocatalysis at low temperatures. FEMS Microbiol. Rev. 28 (2004) 25-42
-
(2004)
FEMS Microbiol. Rev.
, vol.28
, pp. 25-42
-
-
Georlette, D.1
Blaise, V.2
Collins, T.3
D'Amico, S.4
Gratia, E.5
Hoyoux, A.6
Marx, J.C.7
Sonan, G.8
Feller, G.9
Gerday, C.10
-
29
-
-
0034159939
-
Cold-adapted enzymes: from fundamentals to biotechnology
-
Gerday C., Aittaleb M., Bentahir M., Chessa J.P., Claverie P., Collins T., D'Amico S., Dumont J., Garsoux G., Georlette D., et al. Cold-adapted enzymes: from fundamentals to biotechnology. Trends Biotechnol. 18 (2000) 103-107
-
(2000)
Trends Biotechnol.
, vol.18
, pp. 103-107
-
-
Gerday, C.1
Aittaleb, M.2
Bentahir, M.3
Chessa, J.P.4
Claverie, P.5
Collins, T.6
D'Amico, S.7
Dumont, J.8
Garsoux, G.9
Georlette, D.10
-
30
-
-
33646740974
-
Antagonists to human and mouse vascular endothelial growth factor receptor 2 generated by directed protein evolution in vitro
-
Getmanova E.V., Chen Y., Bloom L., Gokemeijer J., Shamah S., Warikoo V., Wang J., Ling V., and Sun L. Antagonists to human and mouse vascular endothelial growth factor receptor 2 generated by directed protein evolution in vitro. Chem. Biol. 13 (2006) 549-556
-
(2006)
Chem. Biol.
, vol.13
, pp. 549-556
-
-
Getmanova, E.V.1
Chen, Y.2
Bloom, L.3
Gokemeijer, J.4
Shamah, S.5
Warikoo, V.6
Wang, J.7
Ling, V.8
Sun, L.9
-
31
-
-
44849128916
-
Generation of affibody (r) ligands binding interieukin-2 receptor alpha/cd25
-
Gronwall C., Snelders E., Palm A.J., Eriksson F., Herne N., and Stahl S. Generation of affibody (r) ligands binding interieukin-2 receptor alpha/cd25. Biotechnol. Appl. Biochem. 50 (2008) 97-112
-
(2008)
Biotechnol. Appl. Biochem.
, vol.50
, pp. 97-112
-
-
Gronwall, C.1
Snelders, E.2
Palm, A.J.3
Eriksson, F.4
Herne, N.5
Stahl, S.6
-
32
-
-
0038692924
-
Molecular dynamics simulation of the unfolding of the human prion protein domain under low ph and high temperature conditions
-
Gu W., Wang T.T., Zhu J., Shi Y.Y., and Liu H.Y. Molecular dynamics simulation of the unfolding of the human prion protein domain under low ph and high temperature conditions. Biophys. Chem. 104 (2003) 79-94
-
(2003)
Biophys. Chem.
, vol.104
, pp. 79-94
-
-
Gu, W.1
Wang, T.T.2
Zhu, J.3
Shi, Y.Y.4
Liu, H.Y.5
-
33
-
-
0000432120
-
The potential calculation and some applications
-
Alder B., Fernbach S., and Rotenberg M. (Eds), Academic Press, New York/London
-
Hockney R.W. The potential calculation and some applications. In: Alder B., Fernbach S., and Rotenberg M. (Eds). Methods in Computational Physics (1970), Academic Press, New York/London 135-211
-
(1970)
Methods in Computational Physics
, pp. 135-211
-
-
Hockney, R.W.1
-
34
-
-
0029785147
-
Mapping the protein universe
-
Holm L., and Sander C. Mapping the protein universe. Science 273 (1996) 595-602
-
(1996)
Science
, vol.273
, pp. 595-602
-
-
Holm, L.1
Sander, C.2
-
35
-
-
29344448254
-
A new generation of protein display scaffolds for molecular recognition
-
Hosse R.J., Rothe A., and Power B.E. A new generation of protein display scaffolds for molecular recognition. Protein Sci. 15 (2006) 14-27
-
(2006)
Protein Sci.
, vol.15
, pp. 14-27
-
-
Hosse, R.J.1
Rothe, A.2
Power, B.E.3
-
36
-
-
42449111198
-
Stabilization of a beta-hairpin in monomeric alzheimer's amyloid-beta peptide inhibits amyloid formation
-
Hoyer W., Gronwall C., Jonsson A., Stahl S., and Hard T. Stabilization of a beta-hairpin in monomeric alzheimer's amyloid-beta peptide inhibits amyloid formation. Proc. Natl. Acad. Sci. U.S.A. 105 (2008) 5099-5104
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 5099-5104
-
-
Hoyer, W.1
Gronwall, C.2
Jonsson, A.3
Stahl, S.4
Hard, T.5
-
37
-
-
19944408939
-
Extreme catalysts from low-temperature environments
-
Hoyoux A., Blaise V., Collins T., D'Amico S., Gratia E., Huston A.L., Marx J.C., Sonan G., Zeng Y., Feller G., et al. Extreme catalysts from low-temperature environments. J. Biosci. Bioeng. 98 (2004) 317-330
-
(2004)
J. Biosci. Bioeng.
, vol.98
, pp. 317-330
-
-
Hoyoux, A.1
Blaise, V.2
Collins, T.3
D'Amico, S.4
Gratia, E.5
Huston, A.L.6
Marx, J.C.7
Sonan, G.8
Zeng, Y.9
Feller, G.10
-
39
-
-
44949233215
-
How to lose a kink and gain a helix: Ph independent conformational changes of the fusion domains from influenza hemagglutinin in heterogeneous lipid bilayers
-
Jang H., Michaud-Agrawal N., Johnston J.M., and Woolf T.B. How to lose a kink and gain a helix: Ph independent conformational changes of the fusion domains from influenza hemagglutinin in heterogeneous lipid bilayers. Proteins: Struct. Funct. Bioinformatics 72 (2008) 299-312
-
(2008)
Proteins: Struct. Funct. Bioinformatics
, vol.72
, pp. 299-312
-
-
Jang, H.1
Michaud-Agrawal, N.2
Johnston, J.M.3
Woolf, T.B.4
-
40
-
-
0020997912
-
Dictionary of protein secondary structure-pattern-recognition of hydrogen-bonded and geometrical features
-
Kabsch W., and Sander C. Dictionary of protein secondary structure-pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
41
-
-
70349240216
-
Adaptive evolution of p53 thermodynamic stability
-
Khoo K.H., Andreeva A., and Fersht A.R. Adaptive evolution of p53 thermodynamic stability. J. Mol. Biol. 393 (2009) 161-175
-
(2009)
J. Mol. Biol.
, vol.393
, pp. 161-175
-
-
Khoo, K.H.1
Andreeva, A.2
Fersht, A.R.3
-
42
-
-
0035813165
-
High thermostability and lack of cooperative DNA binding distinguish the p63 core domain from the homologous tumor suppressor p53
-
Klein C., Georges G., Kunkele K.P., Huber R., Engh R.A., and Hansen S. High thermostability and lack of cooperative DNA binding distinguish the p63 core domain from the homologous tumor suppressor p53. J. Biol. Chem. 276 (2001) 37390-37401
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 37390-37401
-
-
Klein, C.1
Georges, G.2
Kunkele, K.P.3
Huber, R.4
Engh, R.A.5
Hansen, S.6
-
43
-
-
0037452697
-
Designed to be stable: crystal structure of a consensus ankyrin repeat protein
-
Kohl A., Binz H.K., Forrer P., Stumpp M.T., Pluckthun A., and Grutter M.G. Designed to be stable: crystal structure of a consensus ankyrin repeat protein. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 1700-1705
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 1700-1705
-
-
Kohl, A.1
Binz, H.K.2
Forrer, P.3
Stumpp, M.T.4
Pluckthun, A.5
Grutter, M.G.6
-
44
-
-
34547457742
-
Antibody mimics based on the scaffold of the fibronectin type iii domain
-
Koide A., Koide S., and Monobodies:. Antibody mimics based on the scaffold of the fibronectin type iii domain. Methods Mol. Biol. 352 (2007) 95-109
-
(2007)
Methods Mol. Biol.
, vol.352
, pp. 95-109
-
-
Koide, A.1
Koide, S.2
-
45
-
-
34249780547
-
Molecular dynamics simulations of the native and partially folded states of ubiquitin: influence of methanol cosolvent, ph, and temperature on the protein structure and dynamics
-
Kony D.B., Hunenberger P.H., and van Gunsteren W.F. Molecular dynamics simulations of the native and partially folded states of ubiquitin: influence of methanol cosolvent, ph, and temperature on the protein structure and dynamics. Protein Sci. 16 (2007) 1101-1118
-
(2007)
Protein Sci.
, vol.16
, pp. 1101-1118
-
-
Kony, D.B.1
Hunenberger, P.H.2
van Gunsteren, W.F.3
-
46
-
-
0032584722
-
Protein folding stability can determine the efficiency of escape from endoplasmic reticulum quality control
-
Kowalski J.M., Parekh R.N., Mao J., and Wittrup K.D. Protein folding stability can determine the efficiency of escape from endoplasmic reticulum quality control. J. Biol. Chem. 273 (1998) 19453-19458
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 19453-19458
-
-
Kowalski, J.M.1
Parekh, R.N.2
Mao, J.3
Wittrup, K.D.4
-
47
-
-
1342324030
-
Exploring folding free energy landscapes using computational protein design
-
Kuhlman B., and Baker D. Exploring folding free energy landscapes using computational protein design. Curr. Opin. Struct. Biol. 14 (2004) 89-95
-
(2004)
Curr. Opin. Struct. Biol.
, vol.14
, pp. 89-95
-
-
Kuhlman, B.1
Baker, D.2
-
48
-
-
0345306764
-
Design of a novel globular protein fold with atomic-level accuracy
-
Kuhlman B., Dantas G., Ireton G.C., Varani G., Stoddard B.L., and Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science 302 (2003) 1364-1368
-
(2003)
Science
, vol.302
, pp. 1364-1368
-
-
Kuhlman, B.1
Dantas, G.2
Ireton, G.C.3
Varani, G.4
Stoddard, B.L.5
Baker, D.6
-
49
-
-
0030472210
-
Relationship between thermal stability, degradation rate and expression yield of barnase variants in the periplasm of Escherichia coli
-
Kwon W.S., Da Silva N.A., and Kellis J.T. Relationship between thermal stability, degradation rate and expression yield of barnase variants in the periplasm of Escherichia coli. Protein Eng. Des. Sel. 9 (1996) 1197-1202
-
(1996)
Protein Eng. Des. Sel.
, vol.9
, pp. 1197-1202
-
-
Kwon, W.S.1
Da Silva, N.A.2
Kellis, J.T.3
-
50
-
-
0037235978
-
The molecular basis of the temperature- and ph-induced conformational transitions in elastin-based peptides
-
Li B., and Daggett V. The molecular basis of the temperature- and ph-induced conformational transitions in elastin-based peptides. Biopolymers 68 (2003) 121-129
-
(2003)
Biopolymers
, vol.68
, pp. 121-129
-
-
Li, B.1
Daggett, V.2
-
52
-
-
48649094750
-
Fully human antibodies from transgenic mouse and phage display platforms
-
Lonberg N. Fully human antibodies from transgenic mouse and phage display platforms. Curr. Opin. Immunol. 20 (2008) 450-459
-
(2008)
Curr. Opin. Immunol.
, vol.20
, pp. 450-459
-
-
Lonberg, N.1
-
53
-
-
55549108089
-
Engineered enzymes for chemical production
-
Luetz S., Giver L., and Lalonde J. Engineered enzymes for chemical production. Biotechnol. Bioeng. 101 (2008) 647-653
-
(2008)
Biotechnol. Bioeng.
, vol.101
, pp. 647-653
-
-
Luetz, S.1
Giver, L.2
Lalonde, J.3
-
54
-
-
0029828233
-
Strategies for achieving high-level expression of genes in Escherichia coli
-
Makrides S.C. Strategies for achieving high-level expression of genes in Escherichia coli. Microbiol. Rev. 60 (1996) 512-538
-
(1996)
Microbiol. Rev.
, vol.60
, pp. 512-538
-
-
Makrides, S.C.1
-
55
-
-
34249947092
-
Cold-adapted enzymes from marine antarctic microorganisms
-
Marx J.C., Collins T., D'Amico S., Feller G., and Gerday C. Cold-adapted enzymes from marine antarctic microorganisms. Mar. Biotechnol. (NY) 9 (2007) 293-304
-
(2007)
Mar. Biotechnol. (NY)
, vol.9
, pp. 293-304
-
-
Marx, J.C.1
Collins, T.2
D'Amico, S.3
Feller, G.4
Gerday, C.5
-
56
-
-
34547687667
-
Correlation of levels of folded recombinant p53 in Escherichia coli with thermodynamic stability in vitro
-
Mayer S., Rudiger S., Ang H.C., Joerger A.C., and Fersht A.R. Correlation of levels of folded recombinant p53 in Escherichia coli with thermodynamic stability in vitro. J. Mol. Biol. 372 (2007) 268-276
-
(2007)
J. Mol. Biol.
, vol.372
, pp. 268-276
-
-
Mayer, S.1
Rudiger, S.2
Ang, H.C.3
Joerger, A.C.4
Fersht, A.R.5
-
57
-
-
54849406976
-
Display scaffolds: protein engineering for novel therapeutics
-
Nuttall S.D., and Walsh R.B. Display scaffolds: protein engineering for novel therapeutics. Curr. Opin. Pharmacol. 8 (2008) 609-615
-
(2008)
Curr. Opin. Pharmacol.
, vol.8
, pp. 609-615
-
-
Nuttall, S.D.1
Walsh, R.B.2
-
58
-
-
3142677981
-
Binding proteins from alternative scaffolds
-
Nygren P.A., and Skerra A. Binding proteins from alternative scaffolds. J. Immunol. Methods 290 (2004) 3-28
-
(2004)
J. Immunol. Methods
, vol.290
, pp. 3-28
-
-
Nygren, P.A.1
Skerra, A.2
-
60
-
-
0024363466
-
Amino acid substitutions that increase the thermal stability of the lambda cro protein
-
Pakula A.A., and Sauer R.T. Amino acid substitutions that increase the thermal stability of the lambda cro protein. Proteins: Struct. Funct. Bioinf. 5 (1989) 202-210
-
(1989)
Proteins: Struct. Funct. Bioinf.
, vol.5
, pp. 202-210
-
-
Pakula, A.A.1
Sauer, R.T.2
-
61
-
-
29344458564
-
Simulation of ph-dependent edge strand rearrangement in human beta-2 microglobulin
-
Park S., and Saven J.G. Simulation of ph-dependent edge strand rearrangement in human beta-2 microglobulin. Protein Sci. 15 (2006) 200-207
-
(2006)
Protein Sci.
, vol.15
, pp. 200-207
-
-
Park, S.1
Saven, J.G.2
-
62
-
-
70349970427
-
Dynamic properties of a psychrophilic alpha-amylase in comparison with a mesophilic homologue
-
Pasi M., Riccardi L., Fantucci P., De Gioia L., and Papaleo E. Dynamic properties of a psychrophilic alpha-amylase in comparison with a mesophilic homologue. J. Phys. Chem. B 113 (2009) 13585-13595
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 13585-13595
-
-
Pasi, M.1
Riccardi, L.2
Fantucci, P.3
De Gioia, L.4
Papaleo, E.5
-
63
-
-
40549119464
-
The p73 DNA binding domain displays enhanced stability relative to its homologue, the tumor suppressor p53, and exhibits cooperative DNA binding
-
Patel S., Bui T.T.T., Drake A.F., Fraternali F., and Nikolova P.V. The p73 DNA binding domain displays enhanced stability relative to its homologue, the tumor suppressor p53, and exhibits cooperative DNA binding. Biochemistry 47 (2008) 3235-3244
-
(2008)
Biochemistry
, vol.47
, pp. 3235-3244
-
-
Patel, S.1
Bui, T.T.T.2
Drake, A.F.3
Fraternali, F.4
Nikolova, P.V.5
-
64
-
-
34247876138
-
Outlook-development trends for monoclonal antibody cancer therapeutics
-
Reichert J.M., and Valge-Archer V.E. Outlook-development trends for monoclonal antibody cancer therapeutics. Nat. Rev. Drug Discov. 6 (2007) 349-356
-
(2007)
Nat. Rev. Drug Discov.
, vol.6
, pp. 349-356
-
-
Reichert, J.M.1
Valge-Archer, V.E.2
-
65
-
-
33749328523
-
In vitro display technologies reveal novel biopharmaceutics
-
Rothe A., Hosse R.J., and Power B.E. In vitro display technologies reveal novel biopharmaceutics. FASEB J. 20 (2006) 1599-1610
-
(2006)
FASEB J.
, vol.20
, pp. 1599-1610
-
-
Rothe, A.1
Hosse, R.J.2
Power, B.E.3
-
66
-
-
33646940952
-
Numerical-integration of cartesian equations of motion of a system with constraints-molecular-dynamics of n-alkanes
-
Ryckaert J.P., Ciccotti G., and Berendsen H.J.C. Numerical-integration of cartesian equations of motion of a system with constraints-molecular-dynamics of n-alkanes. J. Comp. Phys. 23 (1977) 327-341
-
(1977)
J. Comp. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
67
-
-
1842635571
-
Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection
-
Scalley-Kim M., and Baker D. Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection. J. Mol. Biol. 338 (2004) 573-583
-
(2004)
J. Mol. Biol.
, vol.338
, pp. 573-583
-
-
Scalley-Kim, M.1
Baker, D.2
-
68
-
-
34547151186
-
Single-molecule force spectroscopy reveals a mechanically stable protein fold and the rational tuning of its mechanical stability
-
Sharma D., Perisic O., Peng Q., Cao Y., Lam C., Lu H., and Li H. Single-molecule force spectroscopy reveals a mechanically stable protein fold and the rational tuning of its mechanical stability. Proc. Natl. Acad. Sci. U.S.A. 104 (2007) 9278-9283
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 9278-9283
-
-
Sharma, D.1
Perisic, O.2
Peng, Q.3
Cao, Y.4
Lam, C.5
Lu, H.6
Li, H.7
-
69
-
-
34147174947
-
Pharma consolidates its grip on post-antibody landscape
-
Sheridan C. Pharma consolidates its grip on post-antibody landscape. Nat. Biotechnol. 25 (2007) 365-366
-
(2007)
Nat. Biotechnol.
, vol.25
, pp. 365-366
-
-
Sheridan, C.1
-
70
-
-
24344486447
-
The active site is the least stable structure in the unfolding pathway of a multidomain cold-adapted alpha-amylase
-
Siddiqui K.S., Feller G., D'Amico S., Gerday C., Giaquinto L., and Cavicchioli R. The active site is the least stable structure in the unfolding pathway of a multidomain cold-adapted alpha-amylase. J. Bacteriol. 187 (2005) 6197-6205
-
(2005)
J. Bacteriol.
, vol.187
, pp. 6197-6205
-
-
Siddiqui, K.S.1
Feller, G.2
D'Amico, S.3
Gerday, C.4
Giaquinto, L.5
Cavicchioli, R.6
-
71
-
-
28644436100
-
Multivalent avimer proteins evolved by exon shuffling of a family of human receptor domains
-
Silverman J., Lu Q., Bakker A., To W., Duguay A., Alba B.M., Smith R., Rivas A., Li P., Le H., et al. Multivalent avimer proteins evolved by exon shuffling of a family of human receptor domains. Nat. Biotechnol. 23 (2005) 1556-1561
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 1556-1561
-
-
Silverman, J.1
Lu, Q.2
Bakker, A.3
To, W.4
Duguay, A.5
Alba, B.M.6
Smith, R.7
Rivas, A.8
Li, P.9
Le, H.10
-
72
-
-
32344436215
-
Multivalent avimer proteins evolved by exon shuffling of a family of human receptor domains (vol 23, pg 1556, 2005)
-
Silverman J., Lu Q., Bakker A., To W., Duguay A., Alba B.M., Smith R., Rivas A., Li P., Le H., et al. Multivalent avimer proteins evolved by exon shuffling of a family of human receptor domains (vol 23, pg 1556, 2005). Nat. Biotechnol. 24 (2006) 220-1220
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 220-1220
-
-
Silverman, J.1
Lu, Q.2
Bakker, A.3
To, W.4
Duguay, A.5
Alba, B.M.6
Smith, R.7
Rivas, A.8
Li, P.9
Le, H.10
-
73
-
-
0033865190
-
Engineered protein scaffolds for molecular recognition
-
Skerra A. Engineered protein scaffolds for molecular recognition. J. Mol. Recogn. 13 (2000) 167-187
-
(2000)
J. Mol. Recogn.
, vol.13
, pp. 167-187
-
-
Skerra, A.1
-
74
-
-
0344033650
-
Imitating the humoral immune response
-
Skerra A. Imitating the humoral immune response. Curr. Opin. Chem. Biol. 7 (2003) 683-693
-
(2003)
Curr. Opin. Chem. Biol.
, vol.7
, pp. 683-693
-
-
Skerra, A.1
-
75
-
-
3843129852
-
Alpha- and beta-polypeptides show a different stability of helical secondary structure
-
Soares T., Christen M., Hu K.F., and van Gunsteren W.F. Alpha- and beta-polypeptides show a different stability of helical secondary structure. Tetrahedron 60 (2004) 7775-7780
-
(2004)
Tetrahedron
, vol.60
, pp. 7775-7780
-
-
Soares, T.1
Christen, M.2
Hu, K.F.3
van Gunsteren, W.F.4
-
76
-
-
34248147938
-
Comparative md analysis of the stability of transthyretin providing insight into the fibrillation mechanism
-
Sorensen J., Hamelberg D., Schiott B., and McCammon J.A. Comparative md analysis of the stability of transthyretin providing insight into the fibrillation mechanism. Biopolymers 86 (2007) 73-82
-
(2007)
Biopolymers
, vol.86
, pp. 73-82
-
-
Sorensen, J.1
Hamelberg, D.2
Schiott, B.3
McCammon, J.A.4
-
77
-
-
47349122701
-
The nmr solution structure of the artificial protein m7 matches the computationally designed model
-
Stordeur C., Dalluege R., Birkenmeier O., Wienk H., Rudolph R., Lange C., and Luecke C. The nmr solution structure of the artificial protein m7 matches the computationally designed model. Proteins: Struct. Funct. Bioinformatics 72 (2008) 1104-1107
-
(2008)
Proteins: Struct. Funct. Bioinformatics
, vol.72
, pp. 1104-1107
-
-
Stordeur, C.1
Dalluege, R.2
Birkenmeier, O.3
Wienk, H.4
Rudolph, R.5
Lange, C.6
Luecke, C.7
-
78
-
-
0242338386
-
-
Pacific Northwest National Laboratory, Richland, WA
-
Straatsma T.P., Aprà E., Windus T.L., Bylaska E.J., de Jong W., Hirata S., Valiev M., Hackler M., Pollack L., Harrison R., et al. Nwchem, a Computational Chemistry Package for Parallel Computers, Version 4.6 (2004), Pacific Northwest National Laboratory, Richland, WA
-
(2004)
Nwchem, a Computational Chemistry Package for Parallel Computers, Version 4.6
-
-
Straatsma, T.P.1
Aprà, E.2
Windus, T.L.3
Bylaska, E.J.4
de Jong, W.5
Hirata, S.6
Valiev, M.7
Hackler, M.8
Pollack, L.9
Harrison, R.10
-
79
-
-
27344443434
-
Ph-dependent conformational flexibility of the sars-cov main proteinase (m-pro) dimer: molecular dynamics simulations and multiple X-ray structure analyses
-
Tan J.Z., Verschueren K.H.G., Anand K., Shen J.H., Yang M.J., Xu Y.C., Rao Z.H., Bigalke J., Heisen B., Mesters J.R., et al. Ph-dependent conformational flexibility of the sars-cov main proteinase (m-pro) dimer: molecular dynamics simulations and multiple X-ray structure analyses. J. Mol. Biol. 354 (2005) 25-40
-
(2005)
J. Mol. Biol.
, vol.354
, pp. 25-40
-
-
Tan, J.Z.1
Verschueren, K.H.G.2
Anand, K.3
Shen, J.H.4
Yang, M.J.5
Xu, Y.C.6
Rao, Z.H.7
Bigalke, J.8
Heisen, B.9
Mesters, J.R.10
-
81
-
-
0035650033
-
Molecular dynamics simulation of biomolecular systems
-
van Gunsteren W., Bakowies D., Burgi R., Chandrasekhar I., Christen M., Daura X., Gee P., Glattli A., Hansson T., Oostenbrink C., et al. Molecular dynamics simulation of biomolecular systems. Chimia 55 (2001) 856-860
-
(2001)
Chimia
, vol.55
, pp. 856-860
-
-
van Gunsteren, W.1
Bakowies, D.2
Burgi, R.3
Chandrasekhar, I.4
Christen, M.5
Daura, X.6
Gee, P.7
Glattli, A.8
Hansson, T.9
Oostenbrink, C.10
-
82
-
-
33746271105
-
Biomolecular modeling: goals, problems, perspectives
-
van Gunsteren W.F., Bakowies D., Baron R., Chandrasekhar I., Christen M., Daura X., Gee P., Geerke D.P., Glattli A., Hunenberger P.H., et al. Biomolecular modeling: goals, problems, perspectives. Angew. Chem. Int. Ed. 45 (2006) 4064-4092
-
(2006)
Angew. Chem. Int. Ed.
, vol.45
, pp. 4064-4092
-
-
van Gunsteren, W.F.1
Bakowies, D.2
Baron, R.3
Chandrasekhar, I.4
Christen, M.5
Daura, X.6
Gee, P.7
Geerke, D.P.8
Glattli, A.9
Hunenberger, P.H.10
-
83
-
-
0023380976
-
Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry
-
van Gunsteren W.F., and Berendsen H.J. Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry. J. Comput. Aided Mol. Des. 1 (1987) 171-176
-
(1987)
J. Comput. Aided Mol. Des.
, vol.1
, pp. 171-176
-
-
van Gunsteren, W.F.1
Berendsen, H.J.2
-
85
-
-
0030627407
-
Recovery of protein structure from contact maps
-
Vendruscolo M., Kussell E., and Domany E. Recovery of protein structure from contact maps. Fold. Des. 2 (1997) 295-306
-
(1997)
Fold. Des.
, vol.2
, pp. 295-306
-
-
Vendruscolo, M.1
Kussell, E.2
Domany, E.3
-
86
-
-
33846708445
-
The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection
-
Watters A.L., Deka P., Corrent C., Callender D., Varani G., Sosnick T., and Baker D. The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection. Cell (2007) 128
-
(2007)
Cell
, pp. 128
-
-
Watters, A.L.1
Deka, P.2
Corrent, C.3
Callender, D.4
Varani, G.5
Sosnick, T.6
Baker, D.7
-
87
-
-
0037470646
-
Protein dynamics in a family of laboratory evolved thermophilic enzymes
-
Wintrode P.L., Zhang D.Q., Vaidehi N., Arnold F.H., and Goddard W.A. Protein dynamics in a family of laboratory evolved thermophilic enzymes. J. Mol. Biol. 327 (2003) 745-757
-
(2003)
J. Mol. Biol.
, vol.327
, pp. 745-757
-
-
Wintrode, P.L.1
Zhang, D.Q.2
Vaidehi, N.3
Arnold, F.H.4
Goddard, W.A.5
-
88
-
-
0037188507
-
Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction
-
Xiang Z., Soto C.S., and Honig B. Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 7432-7437
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 7432-7437
-
-
Xiang, Z.1
Soto, C.S.2
Honig, B.3
-
89
-
-
3042616027
-
Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: a molecular dynamics study
-
Yu H.B., Amann M., Hansson T., Kohler J., Wich G., and van Gunsteren W.F. Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: a molecular dynamics study. Carbohydr. Res. 339 (2004) 1697-1709
-
(2004)
Carbohydr. Res.
, vol.339
, pp. 1697-1709
-
-
Yu, H.B.1
Amann, M.2
Hansson, T.3
Kohler, J.4
Wich, G.5
van Gunsteren, W.F.6
-
90
-
-
18044401046
-
Did psychrophilic enzymes really win the challenge?
-
Zecchinon L., Claverie P., Collins T., D'Amico S., Delille D., Feller G., Georlette D., Gratia E., Hoyoux A., Meuwis M.A., et al. Did psychrophilic enzymes really win the challenge?. Extremophiles 5 (2001) 313-321
-
(2001)
Extremophiles
, vol.5
, pp. 313-321
-
-
Zecchinon, L.1
Claverie, P.2
Collins, T.3
D'Amico, S.4
Delille, D.5
Feller, G.6
Georlette, D.7
Gratia, E.8
Hoyoux, A.9
Meuwis, M.A.10
|