-
1
-
-
0021108287
-
Molecular technology-designing proteins and peptides
-
Pabo C (1983) Molecular technology-designing proteins and peptides. Nature 301:200-1200
-
(1983)
Nature
, vol.301
, pp. 200-1200
-
-
Pabo, C.1
-
2
-
-
0023155210
-
Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes
-
DOI 10.1016/0022-2836(87)90358-5
-
Ponder JW, Richards FM (1987) Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol 193:775-791. (Pubitemid 17020078)
-
(1987)
Journal of Molecular Biology
, vol.193
, Issue.4
, pp. 775-791
-
-
Ponder, J.W.1
Richards, F.M.2
-
3
-
-
0032553587
-
High-resolution protein design with backbone freedom
-
Harbury PB, Plecs JJ, Tidor B, Alber T, Kim PS (1998) High-resolution protein design with backbone freedom. Science 282:1462-1467. (Pubitemid 28538602)
-
(1998)
Science
, vol.282
, Issue.5393
, pp. 1462-1467
-
-
Harbury, P.B.1
Plecs, J.J.2
Tidor, B.3
Alber, T.4
Kim, P.S.5
-
4
-
-
0345306764
-
Design of a Novel Globular Protein Fold with Atomic-Level Accuracy
-
DOI 10.1126/science.1089427
-
Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302:1364-1368. (Pubitemid 37452172)
-
(2003)
Science
, vol.302
, Issue.5649
, pp. 1364-1368
-
-
Kuhlman, B.1
Dantas, G.2
Ireton, G.C.3
Varani, G.4
Stoddard, B.L.5
Baker, D.6
-
5
-
-
0030793767
-
De novo protein design: Fully automated sequence selection
-
DOI 10.1126/science.278.5335.82
-
Dahiyat BI, Mayo SL (1997) De novo protein design: fully automated sequence selection. Science 278:82-87. (Pubitemid 27446279)
-
(1997)
Science
, vol.278
, Issue.5335
, pp. 82-87
-
-
Dahiyat, B.I.1
Mayo, S.L.2
-
6
-
-
0031779918
-
Design, structure and stability of a hyperthermophilic protein variant
-
DOI 10.1038/nsb0698-470
-
Malakauskas SM, Mayo SL (1998) Design, structure, and stability of a hyperthermophilic protein variant. Nat Struct Biol 5:470-475. (Pubitemid 28265030)
-
(1998)
Nature Structural Biology
, vol.5
, Issue.6
, pp. 470-475
-
-
Malakauskas, S.M.1
Mayo, S.L.2
-
7
-
-
0041387567
-
A large scale test of computational protein design: Folding and stability of nine completely redesigned globular proteins
-
DOI 10.1016/S0022-2836(03)00888-X
-
Dantas G, Kuhlman B, Callender D, Wong M, Baker D (2003) A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. J Mol Biol 332:449-460. (Pubitemid 37013512)
-
(2003)
Journal of Molecular Biology
, vol.332
, Issue.2
, pp. 449-460
-
-
Dantas, G.1
Kuhlman, B.2
Callender, D.3
Wong, M.4
Baker, D.5
-
8
-
-
34547691430
-
Full-sequence Computational Design and Solution Structure of a Thermostable Protein Variant
-
DOI 10.1016/j.jmb.2007.06.032, PII S0022283607008248
-
Shah PS, Hom GK, Ross SA, Lassila JK, Crowhurst KA, Mayo SL (2007) Full-sequence computational design and solution structure of a thermostable protein variant. J Mol Biol 372:1-6. (Pubitemid 47223220)
-
(2007)
Journal of Molecular Biology
, vol.372
, Issue.1
, pp. 1-6
-
-
Shah, P.S.1
Hom, G.K.2
Ross, S.A.3
Lassila, J.K.4
Crowhurst, K.A.5
Mayo, S.L.6
-
9
-
-
0023007337
-
Computer-aided model-building strategies for protein design
-
DOI 10.1021/bi00368a023
-
Pabo CO, Suchanek EG (1986) Computer-aided model-building strategies for protein design. Biochemistry 25:5987-5991. (Pubitemid 17204033)
-
(1986)
Biochemistry
, vol.25
, Issue.20
, pp. 5987-5991
-
-
Pabo, C.O.1
Suchanek, E.G.2
-
10
-
-
0023006133
-
An engineered intersubunit disulfide enhances the stability and DNA binding of the N-terminal domain of lambda repressor
-
DOI 10.1021/bi00368a024
-
Sauer RT, Hehir K, Stearman RS, Weiss MA, Jeitler-Nilsson A, Suchanek EG, Pabo CO (1986) An engineered intersubunit disulfide enhances the stability and DNA binding of the N-terminal domain of lambda repressor. Biochemistry 25:5992-5998. (Pubitemid 17204034)
-
(1986)
Biochemistry
, vol.25
, Issue.20
, pp. 5992-5998
-
-
Sauer, R.T.1
Hehir, K.2
Stearman, R.S.3
-
11
-
-
0026321752
-
Construction of new ligand binding sites in proteins of known structure. II. Grafting of a buried transition metal binding site into Escherichia coli thioredoxin
-
Hellinga HW, Caradonna JP, Richards FM (1991) Construction of new ligand binding sites in proteins of known structure. II. Grafting of a buried transition metal binding site into Escherichia coli thioredoxin. J Mol Biol 222:787-803.
-
(1991)
J Mol Biol
, vol.222
, pp. 787-803
-
-
Hellinga, H.W.1
Caradonna, J.P.2
Richards, F.M.3
-
14
-
-
0032546610
-
Construction of a novel redox protein by rational design: Conversion of a disulfide bridge into a mononuclear iron-sulfur center
-
DOI 10.1021/bi980583d
-
Benson DE, Wisz MS, Liu W, Hellinga HW (1998) Construction of a novel redox protein by rational design: conversion of a disulfide bridge into a mononuclear iron-sulfur center. Biochemistry 37:7070-7076. (Pubitemid 28235185)
-
(1998)
Biochemistry
, vol.37
, Issue.20
, pp. 7070-7076
-
-
Benson, D.E.1
Wisz, M.S.2
Liu, W.3
Hellinga, H.W.4
-
15
-
-
0032499535
-
2 zinc binding sites in the hydrophobic core of thioredoxin by structure-based design
-
DOI 10.1021/bi980718f
-
Wisz MS, Garrett CZ, Hellinga HW (1998) Construction of a family of Cys2His2 zinc binding sites in the hydrophobic core of thioredoxin by structure-based design. Biochemistry 37:8269-8277. (Pubitemid 28275445)
-
(1998)
Biochemistry
, vol.37
, Issue.23
, pp. 8269-8277
-
-
Wisz, M.S.1
Garrett, C.Z.2
Hellinga, H.W.3
-
16
-
-
0037022813
-
Converting a maltose receptor into a nascent binuclear copper oxygenase by computational design
-
DOI 10.1021/bi011359i
-
Benson DE, Haddy AE, Hellinga HW (2002) Converting a maltose receptor into a nascent binuclear copper oxygenase by computational design. Biochemistry 41:3262-3269. (Pubitemid 34184656)
-
(2002)
Biochemistry
, vol.41
, Issue.9
, pp. 3262-3269
-
-
Benson, D.E.1
Haddy, A.E.2
Hellinga, H.W.3
-
17
-
-
13944256616
-
A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces
-
Jiang L, Kuhlman B, Kortemme TA, Baker D (2005) A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins 58:893-904.
-
(2005)
Proteins
, vol.58
, pp. 893-904
-
-
Jiang, L.1
Kuhlman, B.2
Kortemme, T.A.3
Baker, D.4
-
18
-
-
43449098518
-
Kemp elimination catalysts by computational enzyme design
-
Rothlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS, Baker D (2008) Kemp elimination catalysts by computational enzyme design. Nature 453:190-195.
-
(2008)
Nature
, vol.453
, pp. 190-195
-
-
Rothlisberger, D.1
Khersonsky, O.2
Wollacott, A.M.3
Jiang, L.4
Dechancie, J.5
Betker, J.6
Gallaher, J.L.7
Althoff, E.A.8
Zanghellini, A.9
Dym, O.10
Albeck, S.11
Houk, K.N.12
Tawfik, D.S.13
Baker, D.14
-
19
-
-
0003845223
-
-
San Carlos, CA: DeLano Scientific. Available at: accessed June 2008
-
Delano WL (2002). The PyMOL molecular graphics system. San Carlos, CA: DeLano Scientific. Available at: http:/www.pymol.org. accessed June 2008.
-
(2002)
The PyMOL Molecular Graphics System
-
-
Delano, W.L.1
-
20
-
-
0035393302
-
Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
-
Luscombe NM, Laskowski RA, Thornton JM (2001) Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res 29:2860-2874. (Pubitemid 32685051)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.13
, pp. 2860-2874
-
-
Luscombe, N.M.1
Laskowski, R.A.2
Thornton, J.M.3
-
21
-
-
0347755630
-
AANT: The Amino Acid-Nucleotide Interaction Database
-
Hoffman MM, Khrapov MA, Cox JC, Yao J, Tong L, Ellington AD (2004) AANT: the amino acid-nucleotide interaction database. Nucleic Acids Res 32:D174-D181. (Pubitemid 38081633)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.DATABASE ISS
-
-
Hoffman, M.M.1
Khrapov, M.A.2
Cox, J.C.3
Yao, J.4
Tong, L.5
Ellington, A.D.6
-
22
-
-
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. (Pubitemid 30047768)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, 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
-
23
-
-
33751525692
-
New algorithms and an in silico benchmark for computational enzyme design
-
DOI 10.1110/ps.062353106
-
Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, Althoff EA, Rothlisberger D, Baker D (2006) New algorithms and an in silico benchmark for computational enzyme design. Protein Sci 15:2785-2794. (Pubitemid 44833759)
-
(2006)
Protein Science
, vol.15
, Issue.12
, pp. 2785-2794
-
-
Zanghellini, A.1
Jiang, L.2
Wollacott, A.M.3
Cheng, G.4
Meiler, J.5
Althoff, E.A.6
Rothlisberger, D.7
Baker, D.8
-
24
-
-
40449116114
-
De novo computational design of retro-aldol enzymes
-
Jiang L, Althoff EA, Clemente FR, Doyle L, Rothlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF, III, Hilvert D, Houk KN, Stoddard BL, Baker D (2008) De novo computational design of retro-aldol enzymes. Science 319:1387-1391.
-
(2008)
Science
, vol.319
, pp. 1387-1391
-
-
Jiang, L.1
Althoff, E.A.2
Clemente, F.R.3
Doyle, L.4
Rothlisberger, D.5
Zanghellini, A.6
Gallaher, J.L.7
Betker, J.L.8
Tanaka, F.9
Barbas III, C.F.10
Hilvert, D.11
Houk, K.N.12
Stoddard, B.L.13
Baker, D.14
-
25
-
-
0035883706
-
Homing endonucleases: Structural and functional insight into the catalysts of intron/intein mobility
-
Chevalier BS, Stoddard BL (2001) Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility. Nucleic Acids Res 29:3757-3774. (Pubitemid 32910517)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.18
, pp. 3757-3774
-
-
Chevalier, B.S.1
Stoddard, B.L.2
-
26
-
-
0033751632
-
Severe combined immunodeficiencies (SCID)
-
Fischer A (2000) Severe combined immunodeficiencies (SCID). Clin Exp Immunol 122:143-149.
-
(2000)
Clin Exp Immunol
, vol.122
, pp. 143-149
-
-
Fischer, A.1
-
27
-
-
34548505001
-
Coevolution of a Homing Endonuclease and Its Host Target Sequence
-
DOI 10.1016/j.jmb.2007.07.052, PII S0022283607010054
-
Scalley-Kim M, McConnell-Smith A, Stoddard BL (2007) Coevolution of a homing endonuclease and its host target sequence. J Mol Biol 372:1305-1319. (Pubitemid 47374723)
-
(2007)
Journal of Molecular Biology
, vol.372
, Issue.5
, pp. 1305-1319
-
-
Scalley-Kim, M.1
McConnell-Smith, A.2
Stoddard, B.L.3
-
28
-
-
32044456003
-
The backrub motion: How protein backbone shrugs when a sidechain dances
-
DOI 10.1016/j.str.2005.10.007, PII S0969212606000402
-
Davis IW, Arendall WB, III, Richardson DC, Richardson JS (2006) The backrub motion: how protein backbone shrugs when a sidechain dances. Structure 14:265-274. (Pubitemid 43202016)
-
(2006)
Structure
, vol.14
, Issue.2
, pp. 265-274
-
-
Davis, I.W.1
Arendall III, W.B.2
Richardson, D.C.3
Richardson, J.S.4
-
29
-
-
45649084560
-
Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction
-
Smith CA, Kortemme T (2008) Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J Mol Biol 380:742-756.
-
(2008)
J Mol Biol
, vol.380
, pp. 742-756
-
-
Smith, C.A.1
Kortemme, T.2
-
30
-
-
0035066732
-
The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites
-
DOI 10.1038/86181
-
Chevalier BS, Monnat RJ, Jr, Stoddard BL (2001) The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites. Nat Struct Biol 8:312-316. (Pubitemid 32275014)
-
(2001)
Nature Structural Biology
, vol.8
, Issue.4
, pp. 312-316
-
-
Chevalier, B.S.1
Monnat, R.J.2
Stoddard, B.L.3
-
31
-
-
33646363729
-
The structure of I-CeuI homing endonuclease: Evolving asymmetric DNA recognition from a symmetric protein scaffold
-
Spiegel PC, Chevalier B, Sussman D, Turmel M, Lemieux C, Stoddard BL (2006) The structure of I-CeuI homing endonuclease: evolving asymmetric DNA recognition from a symmetric protein scaffold. Structure 14:869-880.
-
(2006)
Structure
, vol.14
, pp. 869-880
-
-
Spiegel, P.C.1
Chevalier, B.2
Sussman, D.3
Turmel, M.4
Lemieux, C.5
Stoddard, B.L.6
-
32
-
-
55949101131
-
Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering
-
Marcaida MJ, Prieto J, Redondo P, Nadra AD, Alibes A, Serrano L, Grizot S, Duchateau P, Paques F, Blanco FJ, Montoya G (2008) Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering. Proc Natl Acad Sci USA 105:16888-16893.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 16888-16893
-
-
Marcaida, M.J.1
Prieto, J.2
Redondo, P.3
Nadra, A.D.4
Alibes, A.5
Serrano, L.6
Grizot, S.7
Duchateau, P.8
Paques, F.9
Blanco, F.J.10
Montoya, G.11
-
33
-
-
0038061526
-
Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI
-
DOI 10.1016/S0022-2836(03)00447-9
-
Chevalier B, Turmel M, Lemieux C, Monnat RJ, Jr, Stoddard BL (2003) Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI. J Mol Biol 329:253-269. (Pubitemid 36561582)
-
(2003)
Journal of Molecular Biology
, vol.329
, Issue.2
, pp. 253-269
-
-
Chevalier, B.1
Turmel, M.2
Lemieux, C.3
Monnat Jr., R.J.4
Stoddard, B.L.5
-
34
-
-
36049029967
-
High-resolution structure prediction and the crystallographic phase problem
-
DOI 10.1038/nature06249, PII NATURE06249
-
Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D (2007) High-resolution structure prediction and the crystallographic phase problem. Nature 450:259-264. (Pubitemid 350100534)
-
(2007)
Nature
, vol.450
, Issue.7167
, pp. 259-264
-
-
Qian, B.1
Raman, S.2
Das, R.3
Bradley, P.4
McCoy, A.J.5
Read, R.J.6
Baker, D.7
-
35
-
-
36749055649
-
Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home
-
DOI 10.1002/prot.21636
-
Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD, Bhat D, Chivian D, Kim DE, Sheffler WH, Malmstrom L, Wollacott AM, Wang C, Andre I, Baker D (2007) Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins 8(69 Suppl):118-128. (Pubitemid 350210119)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.69
, Issue.SUPPL. 8
, pp. 118-128
-
-
Das, R.1
Qian, B.2
Raman, S.3
Vernon, R.4
Thompson, J.5
Bradley, P.6
Khare, S.7
Tyka, M.D.8
Bhat, D.9
Chivian, D.10
Kim, D.E.11
Sheffler, W.H.12
Malmstrom, L.13
Wollacott, A.M.14
Wang, C.15
Andre, I.16
Baker, D.17
-
36
-
-
0000127073
-
Sequence-specific recognition of double helical nucleic acids by proteins
-
Seeman NC, Rosenberg JM, Rich A (1976) Sequence-specific recognition of double helical nucleic acids by proteins. Proc Natl Acad Sci USA 73:804-808.
-
(1976)
Proc Natl Acad Sci USA
, vol.73
, pp. 804-808
-
-
Seeman, N.C.1
Rosenberg, J.M.2
Rich, A.3
-
37
-
-
0024294636
-
Protein-DNA interaction. No code for recognition
-
Matthews BW (1988) Protein-DNA interaction. No code for recognition. Nature 335:294-295.
-
(1988)
Nature
, vol.335
, pp. 294-295
-
-
Matthews, B.W.1
-
38
-
-
0034682882
-
Geometric analysis and comparison of protein-DNA interfaces: Why is there no simple code for recognition?
-
Pabo CO, Nekludova L (2000) Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? J Mol Biol 301:597-624.
-
(2000)
J Mol Biol
, vol.301
, pp. 597-624
-
-
Pabo, C.O.1
Nekludova, L.2
-
39
-
-
7044239239
-
A simple physical model for the prediction and design of protein-DNA interactions
-
DOI 10.1016/j.jmb.2004.09.029, PII S0022283604011696
-
Havranek JJ, Duarte CM, Baker D (2004) A simple physical model for the prediction and design of protein-DNA interactions. J Mol Biol 344:59-70. (Pubitemid 39422374)
-
(2004)
Journal of Molecular Biology
, vol.344
, Issue.1
, pp. 59-70
-
-
Havranek, J.J.1
Duarte, C.M.2
Baker, D.3
-
40
-
-
27244460904
-
Protein-DNA binding specificity predictions with structural models
-
DOI 10.1093/nar/gki875
-
Morozov AV, Havranek JJ, Baker D, Siggia ED (2005) Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res 33:5781-5798. (Pubitemid 41742598)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.18
, pp. 5781-5798
-
-
Morozov, A.V.1
Havranek, J.J.2
Baker, D.3
Siggia, E.D.4
-
41
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
DOI 10.1006/jmbi.1997.0959
-
Simons KT, Kooperberg C, Huang E, Baker D (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 268:209-225. (Pubitemid 27192690)
-
(1997)
Journal of Molecular Biology
, vol.268
, Issue.1
, pp. 209-225
-
-
Simons, K.T.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
-
42
-
-
0037406075
-
Cyclic coordinate descent: A robotics algorithm for protein loop closure
-
DOI 10.1110/ps.0242703
-
Canutescu AA, Dunbrack RL (2003) Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci 12:963-972. (Pubitemid 36505431)
-
(2003)
Protein Science
, vol.12
, Issue.5
, pp. 963-972
-
-
Canutescu, A.A.1
Dunbrack Jr., R.L.2
|