-
1
-
-
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
-
2
-
-
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
-
3
-
-
77954811495
-
Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction
-
Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, St Clair JL, Gallaher JL, Hilvert D, Gelb MH, Stoddard BL, et al. (2010) Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 329:309-313.
-
(2010)
Science
, vol.329
, pp. 309-313
-
-
Siegel, J.B.1
Zanghellini, A.2
Lovick, H.M.3
Kiss, G.4
Lambert, A.R.5
St Clair, J.L.6
Gallaher, J.L.7
Hilvert, D.8
Gelb, M.H.9
Stoddard, B.L.10
-
4
-
-
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
-
5
-
-
34147130190
-
Computational design of peptides that target transmembrane helices
-
DOI 10.1126/science.1136782
-
Yin H, Slusky JS, Berger BW, Walters RS, Vilaire G, Litvinov RI, Lear JD, Caputo GA, Bennett JS, DeGrado WF (2007) Computational design of peptides that target transmembrane helices. Science 315: 1817-1822. (Pubitemid 46580135)
-
(2007)
Science
, vol.315
, Issue.5820
, pp. 1817-1822
-
-
Yin, H.1
Slusky, J.S.2
Berger, B.W.3
Walters, R.S.4
Vilaire, G.5
Litvinov, R.I.6
Lear, J.D.7
Caputo, G.A.8
Bennett, J.S.9
DeGrado, W.F.10
-
6
-
-
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 458:859-864.
-
(2009)
Nature
, vol.458
, pp. 859-864
-
-
Grigoryan, G.1
Reinke, A.W.2
Keating, A.E.3
-
7
-
-
79957589641
-
Computational design of virus-like protein assemblies on carbon nanotube surfaces
-
Grigoryan G, Kim YH, Acharya R, Axelrod K, Jain RM, Willis L, Drndic M, Kikkawa JM, DeGrado WF (2011) Computational design of virus-like protein assemblies on carbon nanotube surfaces. Science 332:1071-1076.
-
(2011)
Science
, vol.332
, pp. 1071-1076
-
-
Grigoryan, G.1
Kim, Y.H.2
Acharya, R.3
Axelrod, K.4
Jain, R.M.5
Willis, L.6
Drndic, M.7
Kikkawa, J.M.8
DeGrado, W.F.9
-
8
-
-
80052334922
-
RosettaRemodel: A generalized framework for flexible backbone protein design
-
Huang PS, Ban YEA, Richter F, Andre I, Vernon R, Schief WR, Baker D (2011) RosettaRemodel: A generalized framework for flexible backbone protein design. PloSOne 6:e24109.
-
(2011)
PloSOne
, vol.6
-
-
Huang, P.S.1
Ban, Y.E.A.2
Richter, F.3
Andre, I.4
Vernon, R.5
Schief, W.R.6
Baker, D.7
-
9
-
-
78650413957
-
Circular permutation: A different way to engineer enzyme structure and function
-
Yu Y, Lutz S (2011) Circular permutation: a different way to engineer enzyme structure and function. Trends Biotechnol 29:18-25.
-
(2011)
Trends Biotechnol
, vol.29
, pp. 18-25
-
-
Yu, Y.1
Lutz, S.2
-
10
-
-
77956317558
-
Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope
-
Correia BE, Ban YE, Holmes MA, Xu H, Ellingson K, Kraft Z, Carrico C, Boni E, Sather DN, Zenobia C, et al. (2010) Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope. Structure 18:1116-1126.
-
(2010)
Structure
, vol.18
, pp. 1116-1126
-
-
Correia, B.E.1
Ban, Y.E.2
Holmes, M.A.3
Xu, H.4
Ellingson, K.5
Kraft, Z.6
Carrico, C.7
Boni, E.8
Sather, D.N.9
Zenobia, C.10
-
11
-
-
34548861782
-
Protein-Protein Docking with Backbone Flexibility
-
DOI 10.1016/j.jmb.2007.07.050, PII S0022283607010030
-
Wang C, Bradley P, Baker D (2007) Protein-protein docking with backbone flexibility. J Mol Biol 373: 503-519. (Pubitemid 47445567)
-
(2007)
Journal of Molecular Biology
, vol.373
, Issue.2
, pp. 503-519
-
-
Wang, C.1
Bradley, P.2
Baker, D.3
-
12
-
-
0037406075
-
Cyclic coordinate descent: A robotics algorithm for protein loop closure
-
DOI 10.1110/ps.0242703
-
Canutescu AA, Dunbrack RL, Jr (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
-
13
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
DOI 10.1093/nar/25.17.3389
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402. (Pubitemid 27359211)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
14
-
-
78149378424
-
Tying up the loose ends: Circular permutation decreases the proteolytic susceptibility of recombinant proteins
-
Whitehead TA, Bergeron LM, Clark DS (2009) Tying up the loose ends: circular permutation decreases the proteolytic susceptibility of recombinant proteins. Protein Eng Des Sel 22:607-613.
-
(2009)
Protein Eng des Sel
, vol.22
, pp. 607-613
-
-
Whitehead, T.A.1
Bergeron, L.M.2
Clark, D.S.3
-
15
-
-
77949506674
-
Circular permutation of Bacillus circulans xylanase: A kinetic and structural study
-
Reitinger S, Yu Y, Wicki J, Ludwiczek M, D'Angelo I, Baturin S, Okon M, Strynadka NC, Lutz S, Withers SG, et al. (2010) Circular permutation of Bacillus circulans xylanase: a kinetic and structural study. Biochemistry 49:2464-2474.
-
(2010)
Biochemistry
, vol.49
, pp. 2464-2474
-
-
Reitinger, S.1
Yu, Y.2
Wicki, J.3
Ludwiczek, M.4
D'Angelo, I.5
Baturin, S.6
Okon, M.7
Strynadka, N.C.8
Lutz, S.9
Withers, S.G.10
-
16
-
-
25844525807
-
Improving the catalytic activity of Candida antarctica lipase B by circular permutation
-
DOI 10.1021/ja053932h
-
Qian Z, Lutz S (2005) Improving the catalytic activity of Candida antarctica lipase B by circular permutation. J Am Chem Soc 127:13466-13467. (Pubitemid 41401178)
-
(2005)
Journal of the American Chemical Society
, vol.127
, Issue.39
, pp. 13466-13467
-
-
Qian, Z.1
Lutz, S.2
-
17
-
-
0042847339
-
Circular permutation of 5-aminolevulinate synthase: Effect on folding, conformational stability, and structure
-
DOI 10.1074/jbc.M207011200
-
Cheltsov AV, Guida WC, Ferreira GC (2003) Circular permutation of 5-aminolevulinate synthase: effect on folding, conformational stability, and structure. J Biol Chem 278:27945-27955. (Pubitemid 36899989)
-
(2003)
Journal of Biological Chemistry
, vol.278
, Issue.30
, pp. 27945-27955
-
-
Cheltsov, A.V.1
Guida, W.C.2
Ferreira, G.C.3
-
18
-
-
36749039234
-
High-resolution design of a protein loop
-
DOI 10.1073/pnas.0707977104
-
Hu X, Wang H, Ke H, Kuhlman B (2007) High-resolution design of a protein loop. Proc Natl Acad Sci USA 104:17668-17673. (Pubitemid 350210892)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.45
, pp. 17668-17673
-
-
Hu, X.1
Wang, H.2
Ke, H.3
Kuhlman, B.4
-
19
-
-
78650414310
-
Computational protein design using flexible backbone remodeling and resurfacing: Case studies in structure-based antigen design
-
Correia BE, Ban YE, Friend DJ, Ellingson K, Xu H, Boni E, Bradley-Hewitt T, Bruhn-Johannsen JF, Stamatatos L, Strong RK, et al. (2011) Computational protein design using flexible backbone remodeling and resurfacing: case studies in structure-based antigen design. J Mol Biol 405:284-297.
-
(2011)
J Mol Biol
, vol.405
, pp. 284-297
-
-
Correia, B.E.1
Ban, Y.E.2
Friend, D.J.3
Ellingson, K.4
Xu, H.5
Boni, E.6
Bradley-Hewitt, T.7
Bruhn-Johannsen, J.F.8
Stamatatos, L.9
Strong, R.K.10
-
20
-
-
50649095790
-
Macromolecular modeling with rosetta
-
Das R, Baker D (2008) Macromolecular modeling with rosetta. Ann Rev Biochem 77:363-382.
-
(2008)
Ann Rev Biochem
, vol.77
, pp. 363-382
-
-
Das, R.1
Baker, D.2
-
22
-
-
0033213239
-
The finer things in X-ray diffraction data collection
-
Pflugrath JW (1999) The finer things in X-ray diffraction data collection. Acta Cryst D55:1718-1725.
-
(1999)
Acta Cryst
, vol.D55
, pp. 1718-1725
-
-
Pflugrath, J.W.1
-
23
-
-
34447508216
-
Phaser crystallographic software
-
DOI 10.1107/S0021889807021206, PII S0021889807021206
-
McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ (2007) Phaser crystallographic software. J Appl Cryst 40:658-674. (Pubitemid 47080256)
-
(2007)
Journal of Applied Crystallography
, vol.40
, Issue.4
, pp. 658-674
-
-
McCoy, A.J.1
Grosse-Kunstleve, R.W.2
Adams, P.D.3
Winn, M.D.4
Storoni, L.C.5
Read, R.J.6
-
24
-
-
0037779018
-
A graphical user interface to the CCP4 program suite
-
DOI 10.1107/S0907444903008126
-
Potterton E, Briggs P, Turkenburg M, Dodson E (2003) A graphical user interface to the CCP4 program suite. Acta Cryst D59:1131-1137. (Pubitemid 36872348)
-
(2003)
Acta Crystallographica Section D: Biological Crystallography
, vol.59
, Issue.7
, pp. 1131-1137
-
-
Potterton, E.1
Briggs, P.2
Turkenburg, M.3
Dodson, E.4
-
27
-
-
0000243829
-
PROCHECK: A program to check the stereochemical quality of protein structures
-
Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26:283-291.
-
(1993)
J Appl Cryst
, vol.26
, pp. 283-291
-
-
Laskowski, R.A.1
MacArthur, M.W.2
Moss, D.S.3
Thornton, J.M.4
-
28
-
-
34547592557
-
MolProbity: All-atom contacts and structure validation for proteins and nucleic acids
-
Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB, III, Snoeyink J, Richardson JS, et al. (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35:W375-W383.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Davis, I.W.1
Leaver-Fay, A.2
Chen, V.B.3
Block, J.N.4
Kapral, G.J.5
Wang, X.6
Murray, L.W.7
Arendall III, W.B.8
Snoeyink, J.9
Richardson, J.S.10
-
29
-
-
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
|