-
1
-
-
0035843136
-
Combinatorial and computational challenges for biocatalyst design
-
Arnold FH (2001) Combinatorial and computational challenges for biocatalyst design. Nature 409(6817):253-257.
-
(2001)
Nature
, vol.409
, Issue.6817
, pp. 253-257
-
-
Arnold, F.H.1
-
2
-
-
43049123356
-
Advances in laboratory evolution of enzymes
-
Bershtein S, Tawfik DS (2008) Advances in laboratory evolution of enzymes. Curr Opin Chem Biol 12(2):151-158.
-
(2008)
Curr Opin Chem Biol
, vol.12
, Issue.2
, pp. 151-158
-
-
Bershtein, S.1
Tawfik, D.S.2
-
4
-
-
27344449197
-
Progress in modeling of protein structures and interactions
-
Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D (2005) Progress in modeling of protein structures and interactions. Science 310(5748):638-642.
-
(2005)
Science
, vol.310
, Issue.5748
, pp. 638-642
-
-
Schueler-Furman, O.1
Wang, C.2
Bradley, P.3
Misura, K.4
Baker, D.5
-
5
-
-
33847731021
-
Computational protein design promises to revolutionize protein engineering
-
Alvizo O, Allen BD, Mayo SL (2007) Computational protein design promises to revolutionize protein engineering. Biotechniques 42(1):31-35.
-
(2007)
Biotechniques
, vol.42
, Issue.1
, pp. 31-35
-
-
Alvizo, O.1
Allen, B.D.2
Mayo, S.L.3
-
6
-
-
34548528158
-
Progress in computational protein design
-
Lippow SM, Tidor B (2007) Progress in computational protein design. Curr Opin Biotech 18(4):305-311.
-
(2007)
Curr Opin Biotech
, vol.18
, Issue.4
, pp. 305-311
-
-
Lippow, S.M.1
Tidor, B.2
-
7
-
-
0030793767
-
De novo protein design: Fully automated sequence selection
-
Dahiyat BI, Mayo SL (1997) De novo protein design: Fully automated sequence selection. Science 278(5335):82-87.
-
(1997)
Science
, vol.278
, Issue.5335
, pp. 82-87
-
-
Dahiyat, B.I.1
Mayo, S.L.2
-
8
-
-
0031779918
-
Design, structure and stability of a hyperthermophilic protein variant
-
Malakauskas SM, Mayo SL (1998) Design, structure and stability of a hyperthermophilic protein variant. Nat Struct Biol 5(6):470-475.
-
(1998)
Nat Struct Biol
, vol.5
, Issue.6
, pp. 470-475
-
-
Malakauskas, S.M.1
Mayo, S.L.2
-
9
-
-
0035807809
-
Enzyme-like proteins by computational design
-
Bolon DN, Mayo SL (2001) Enzyme-like proteins by computational design. Proc Natl Acad Sci USA 98(25):14274-14279.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, Issue.25
, pp. 14274-14279
-
-
Bolon, D.N.1
Mayo, S.L.2
-
10
-
-
0345306764
-
Design of a novel globular protein fold with atomic-level accuracy
-
Kuhlman B, et al. (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302(5649):1364-1368.
-
(2003)
Science
, vol.302
, Issue.5649
, pp. 1364-1368
-
-
Kuhlman, B.1
-
11
-
-
40449116114
-
De novo computational design of retro-aldol enzymes
-
Jiang L, et al. (2008) De novo computational design of retro-aldol enzymes. Science 319(5868):1387-1391.
-
(2008)
Science
, vol.319
, Issue.5868
, pp. 1387-1391
-
-
Jiang, L.1
-
12
-
-
43449098518
-
Kemp elimination catalysts by computational enzyme design
-
Rothlisberger D, et al. (2008) Kemp elimination catalysts by computational enzyme design. Nature 453(7192):190-195.
-
(2008)
Nature
, vol.453
, Issue.7192
, pp. 190-195
-
-
Rothlisberger, D.1
-
13
-
-
23444450226
-
Semi-rational approaches to engineering enzyme activity: Combining the benefits of directed evolution and rational design
-
Chica RA, Doucet N, Pelletier JN (2005) Semi-rational approaches to engineering enzyme activity: Combining the benefits of directed evolution and rational design. Curr Opin Biotech 16(4):378-384.
-
(2005)
Curr Opin Biotech
, vol.16
, Issue.4
, pp. 378-384
-
-
Chica, R.A.1
Doucet, N.2
Pelletier, J.N.3
-
14
-
-
0030032461
-
The denatured state (the other half of the folding equation) and its role in protein stability
-
Shortle D (1996) The denatured state (the other half of the folding equation) and its role in protein stability. FASEB J 10(1):27-34.
-
(1996)
FASEB J
, vol.10
, Issue.1
, pp. 27-34
-
-
Shortle, D.1
-
15
-
-
1842326139
-
Bayesian statistical analysis of protein side-chain rotamer preferences
-
Dunbrack RL, Cohen FE (1997) Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci 6(8):1661-1681.
-
(1997)
Protein Sci
, vol.6
, Issue.8
, pp. 1661-1681
-
-
Dunbrack, R.L.1
Cohen, F.E.2
-
16
-
-
33750963095
-
Combinatorial methods for small- molecule placement in computational enzyme design
-
Lassila JK, Privett HK, Allen BD, Mayo SL (2006) Combinatorial methods for small- molecule placement in computational enzyme design. Proc Natl Acad Sci USA 103(45):16710-16715.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, Issue.45
, pp. 16710-16715
-
-
Lassila, J.K.1
Privett, H.K.2
Allen, B.D.3
Mayo, S.L.4
-
17
-
-
0030987610
-
Probing the role of packing specificity in protein design
-
Dahiyat BI, Mayo SL (1997) Probing the role of packing specificity in protein design. Proc Natl Acad Sci USA 94(19):10172-10177.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, Issue.19
, pp. 10172-10177
-
-
Dahiyat, B.I.1
Mayo, S.L.2
-
18
-
-
34548764385
-
Computing van der Waals energies in the context of the rotamer approximation
-
Grigoryan G, Ochoa A, Keating AE (2007) Computing van der Waals energies in the context of the rotamer approximation. Proteins 68(4):863-878.
-
(2007)
Proteins
, vol.68
, Issue.4
, pp. 863-878
-
-
Grigoryan, G.1
Ochoa, A.2
Keating, A.E.3
-
19
-
-
36749039234
-
High-resolution design of a protein loop
-
Hu X, Wang H, Ke H, Kuhlman B (2007) High-resolution design of a protein loop. Proc Natl Acad Sci USA 104(45):17668-17673.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, Issue.45
, pp. 17668-17673
-
-
Hu, X.1
Wang, H.2
Ke, H.3
Kuhlman, B.4
-
20
-
-
14144256681
-
Energy functions for protein design: Adjustment with protein-protein complexaffinities, models for the unfolded state, and negative design of solubility and specificity
-
Pokala N, Handel TM (2005) Energy functions for protein design: Adjustment with protein-protein complexaffinities, models for the unfolded state, and negative design of solubility and specificity. J Mol Biol 347(1):203-227.
-
(2005)
J Mol Biol
, vol.347
, Issue.1
, pp. 203-227
-
-
Pokala, N.1
Handel, T.M.2
-
21
-
-
0037217406
-
Automated design of specificity in molecular recognition
-
Havranek JJ, Harbury PB (2003) Automated design of specificity in molecular recognition. Nat Struct Biol 10(1):45-52.
-
(2003)
Nat Struct Biol
, vol.10
, Issue.1
, pp. 45-52
-
-
Havranek, J.J.1
Harbury, P.B.2
-
22
-
-
31944435091
-
Computational design of a single amino acid sequence that can switch between two distinct protein folds
-
Ambroggio XI, Kuhlman B (2006) Computational design of a single amino acid sequence that can switch between two distinct protein folds. J Am Chem Soc 128(4):1154-1161.
-
(2006)
J Am Chem Soc
, vol.128
, Issue.4
, pp. 1154-1161
-
-
Ambroggio, X.I.1
Kuhlman, B.2
-
23
-
-
44949229094
-
Design of protein-ligand binding based on the molecular-mechanics energy model
-
Boas FE, Harbury PB (2008) Design of protein-ligand binding based on the molecular-mechanics energy model. J Mol Biol 380(2):415-424.
-
(2008)
J Mol Biol
, vol.380
, Issue.2
, pp. 415-424
-
-
Boas, F.E.1
Harbury, P.B.2
-
24
-
-
77952849163
-
An efficient algorithm for multistate protein design based on FASTER
-
Allen BD, Mayo SL (2010) An efficient algorithm for multistate protein design based on FASTER. J Comput Chem 31:904-916.
-
(2010)
J Comput Chem
, vol.31
, pp. 904-916
-
-
Allen, B.D.1
Mayo, S.L.2
-
25
-
-
0035936702
-
Statistical theory for protein combinatorial libraries. Packing interactions, backbone flexibility, and the sequence variability of a main-chain structure
-
Kono H, Saven JG (2001) Statistical theory for protein combinatorial libraries. Packing interactions, backbone flexibility, and the sequence variability of a main-chain structure. J Mol Biol 306(3):607-628.
-
(2001)
J Mol Biol
, vol.306
, Issue.3
, pp. 607-628
-
-
Kono, H.1
Saven, J.G.2
-
26
-
-
0037059061
-
Combining computational and experimental screening for rapid optimization of protein properties
-
Hayes RJ, et al. (2002) Combining computational and experimental screening for rapid optimization of protein properties. Proc Natl Acad Sci USA 99(25):15926-15931.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, Issue.25
, pp. 15926-15931
-
-
Hayes, R.J.1
-
27
-
-
27944437517
-
Automated design of degenerate codon libraries
-
Mena MA, Daugherty PS (2005) Automated design of degenerate codon libraries. Protein Eng DesSel 18(12):559-561.
-
(2005)
Protein Eng DesSel
, vol.18
, Issue.12
, pp. 559-561
-
-
Mena, M.A.1
Daugherty, P.S.2
-
28
-
-
33846102955
-
Computationally designed libraries of fluorescent proteins evaluated bypreservation and diversity of function
-
Treynor TP, Vizcarra CL, Nedelcu D, Mayo SL (2007) Computationally designed libraries of fluorescent proteins evaluated bypreservation and diversity of function. Proc Natl Acad Sci USA 104(1):48-53.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, Issue.1
, pp. 48-53
-
-
Treynor, T.P.1
Vizcarra, C.L.2
Nedelcu, D.3
Mayo, S.L.4
-
29
-
-
0036829597
-
Core mutations switch monomeric protein GB1 into an intertwined tetramer
-
Kirsten Frank M, Dyda F, Dobrodumov A, Gronenborn AM (2002) Core mutations switch monomeric protein GB1 into an intertwined tetramer. Nat Struct Biol 9(11):877-885.
-
(2002)
Nat Struct Biol
, vol.9
, Issue.11
, pp. 877-885
-
-
Kirsten Frank, M.1
Dyda, F.2
Dobrodumov, A.3
Gronenborn, A.M.4
-
30
-
-
0141569110
-
A protein contortionist: Core mutations of GB1 that induce dimerization and domain swapping
-
Byeon IJ, Louis JM, Gronenborn AM (2003) A protein contortionist: Core mutations of GB1 that induce dimerization and domain swapping. J Mol Biol 333(1):141-152.
-
(2003)
J Mol Biol
, vol.333
, Issue.1
, pp. 141-152
-
-
Byeon, I.J.1
Louis, J.M.2
Gronenborn, A.M.3
-
31
-
-
42449084973
-
The point mutation A34F causes dimerization of GB1
-
Jee J, Byeon IJ, Louis JM, Gronenborn AM (2008) The point mutation A34F causes dimerization of GB1. Proteins 71(3):1420-1431.
-
(2008)
Proteins
, vol.71
, Issue.3
, pp. 1420-1431
-
-
Jee, J.1
Byeon, I.J.2
Louis, J.M.3
Gronenborn, A.M.4
-
32
-
-
0036892389
-
Thoroughly sampling sequence space: Large-scale protein design of structural ensembles
-
Larson SM, England JL, Desjarlais JR, Pande VS (2002) Thoroughly sampling sequence space: Large-scale protein design of structural ensembles. Protein Sci 11(12):2804-2813.
-
(2002)
Protein Sci
, vol.11
, Issue.12
, pp. 2804-2813
-
-
Larson, S.M.1
England, J.L.2
Desjarlais, J.R.3
Pande, V.S.4
-
33
-
-
34547121250
-
Modeling backbone flexibility to achieve sequence diversity: The design of novel alpha-helical ligands for Bcl-xL
-
Fu X, Apgar JR, Keating AE (2007) Modeling backbone flexibility to achieve sequence diversity: The design of novel alpha-helical ligands for Bcl-xL. J Mol Biol 371(4):1099-1117.
-
(2007)
J Mol Biol
, vol.371
, Issue.4
, pp. 1099-1117
-
-
Fu, X.1
Apgar, J.R.2
Keating, A.E.3
-
34
-
-
70349334428
-
X-ray vs.NMR structures as templates for computational protein design
-
Schneider M, Fu X, Keating AE (2009) X-ray vs.NMR structures as templates for computational protein design. Proteins 77(1):97-110.
-
(2009)
Proteins
, vol.77
, Issue.1
, pp. 97-110
-
-
Schneider, M.1
Fu, X.2
Keating, A.E.3
-
35
-
-
9144240095
-
Dreiding-a generic force-field for molecular simulations
-
Mayo SL, Olafson BD, Goddard WA (1990) Dreiding-a generic force-field for molecular simulations. J Phys Chem 94(26):8897-8909.
-
(1990)
J Phys Chem
, vol.94
, Issue.26
, pp. 8897-8909
-
-
Mayo, S.L.1
Olafson, B.D.2
Goddard, W.A.3
-
38
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
-
Guerois R, Nielsen JE, Serrano L (2002) Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations. J Mol Biol 320(2):369-387.
-
(2002)
J Mol Biol
, vol.320
, Issue.2
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
39
-
-
34249777526
-
Eris: An automated estimator of protein stability
-
Yin S, Ding F, Dokholyan NV (2007) Eris: An automated estimator of protein stability. Nat Methods 4(6):466-467.
-
(2007)
Nat Methods
, vol.4
, Issue.6
, pp. 466-467
-
-
Yin, S.1
Ding, F.2
Dokholyan, N.V.3
-
40
-
-
74549207309
-
Assessing computational methods for predicting protein stability upon mutation: Good on average but not in the details
-
Potapov V, Cohen M, Schreiber G (2009) Assessing computational methods for predicting protein stability upon mutation: Good on average but not in the details. Protein Eng Des Sel 22(9):553-560.
-
(2009)
Protein Eng des Sel
, vol.22
, Issue.9
, pp. 553-560
-
-
Potapov, V.1
Cohen, M.2
Schreiber, G.3
-
41
-
-
65249171530
-
Design of protein-interaction specificity gives selective bZIP-binding peptides
-
Grigoryan G, Reinke AW, Keating AE (2009) Design of protein-interaction specificity gives selective bZIP-binding peptides. Nature 458(7240):859-864.
-
(2009)
Nature
, vol.458
, Issue.7240
, pp. 859-864
-
-
Grigoryan, G.1
Reinke, A.W.2
Keating, A.E.3
-
42
-
-
0028354429
-
2 crystal-structures of the B1 immunoglobulin-binding domain of streptococcal protein-G and comparison with Nmr
-
Gallagher T, Alexander P, Bryan P, Gilliland GL (1994) 2 crystal-structures of the B1 immunoglobulin-binding domain of streptococcal protein-G and comparison with Nmr. Biochemistry 33(15):4721-4729.
-
(1994)
Biochemistry
, vol.33
, Issue.15
, pp. 4721-4729
-
-
Gallagher, T.1
Alexander, P.2
Bryan, P.3
Gilliland, G.L.4
-
43
-
-
0025769350
-
A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G
-
Gronenborn AM, et al. (1991) A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G. Science 253(5020):657-661.
-
(1991)
Science
, vol.253
, Issue.5020
, pp. 657-661
-
-
Gronenborn, A.M.1
-
44
-
-
0033614004
-
Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
-
Word JM, Lovell SC, Richardson JS, Richardson DC (1999) Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 285(4):1735-1747.
-
(1999)
J Mol Biol
, vol.285
, Issue.4
, pp. 1735-1747
-
-
Word, J.M.1
Lovell, S.C.2
Richardson, J.S.3
Richardson, D.C.4
-
46
-
-
0037472680
-
Exact rotamer optimization for protein design
-
Gordon DB, Hom GK, Mayo SL, Pierce NA (2003) Exact rotamer optimization for protein design. J Comput Chem 24(2):232-243.
-
(2003)
J Comput Chem
, vol.24
, Issue.2
, pp. 232-243
-
-
Gordon, D.B.1
Hom, G.K.2
Mayo, S.L.3
Pierce, N.A.4
-
47
-
-
33745614865
-
Dramatic performance enhancements for the FASTER optimization algorithm
-
Allen BD, Mayo SL (2006) Dramatic performance enhancements for the FASTER optimization algorithm. J Comput Chem 27(10):1071-1075.
-
(2006)
J Comput Chem
, vol.27
, Issue.10
, pp. 1071-1075
-
-
Allen, B.D.1
Mayo, S.L.2
-
48
-
-
0028784138
-
Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides
-
Stemmer WP, Crameri A, Ha KD, Brennan TM, Heyneker HL (1995) Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene 164(1):49-53.
-
(1995)
Gene
, vol.164
, Issue.1
, pp. 49-53
-
-
Stemmer, W.P.1
Crameri, A.2
Ha, K.D.3
Brennan, T.M.4
Heyneker, H.L.5
-
49
-
-
0043285072
-
A partition function algorithm for nucleic acid secondary structure including pseudoknots
-
Dirks RM, Pierce NA (2003) A partition function algorithm for nucleic acid secondary structure including pseudoknots. J Comput Chem 24(13):1664-1677.
-
(2003)
J Comput Chem
, vol.24
, Issue.13
, pp. 1664-1677
-
-
Dirks, R.M.1
Pierce, N.A.2
-
50
-
-
3042554001
-
An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots
-
Dirks RM, Pierce NA (2004) An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. J Comput Chem 25(10):1295-1304.
-
(2004)
J Comput Chem
, vol.25
, Issue.10
, pp. 1295-1304
-
-
Dirks, R.M.1
Pierce, N.A.2
-
51
-
-
9644259239
-
A second-generation system for unbiased reading frame selection
-
Gerth ML, Patrick WM, Lutz S (2004) A second-generation system for unbiased reading frame selection. Protein Eng Des Sel 17(7):595-602.
-
(2004)
Protein Eng des Sel
, vol.17
, Issue.7
, pp. 595-602
-
-
Gerth, M.L.1
Patrick, W.M.2
Lutz, S.3
-
52
-
-
15944380354
-
High-throughput measurement of protein stability in microtiter plates
-
Aucamp JP, Cosme AM, Lye GJ, Dalby PA (2005) High-throughput measurement of protein stability in microtiter plates. Biotechnol Bioeng 89(5):599-607.
-
(2005)
Biotechnol Bioeng
, vol.89
, Issue.5
, pp. 599-607
-
-
Aucamp, J.P.1
Cosme, A.M.2
Lye, G.J.3
Dalby, P.A.4
-
53
-
-
0023697408
-
Unfolding free energy changes determined by the linear extrapolation method.1. Unfolding of phenylmethanesulfonyl alpha-chymo-trypsin using different denaturants
-
Santoro MM, Bolen DW (1988) Unfolding free energy changes determined by the linear extrapolation method.1. Unfolding of phenylmethanesulfonyl alpha-chymo-trypsin using different denaturants. Biochemistry 27(21):8063-8068.
-
(1988)
Biochemistry
, vol.27
, Issue.21
, pp. 8063-8068
-
-
Santoro, M.M.1
Bolen, D.W.2
|