-
1
-
-
62649153772
-
Computational structure-based redesign of enzyme activity
-
Chen CY, Georgiev I, Anderson AC, Donald BR, (2009) Computational structure-based redesign of enzyme activity. Proc Natl Acad Sci U S A 106: 3764-3769.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 3764-3769
-
-
Chen, C.Y.1
Georgiev, I.2
Anderson, A.C.3
Donald, B.R.4
-
2
-
-
77954811495
-
Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction
-
Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, 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
-
3
-
-
77956377719
-
Predicting resistance mutations using protein design algorithms
-
Frey KM, Georgiev I, Donald BR, Anderson AC, (2010) Predicting resistance mutations using protein design algorithms. Proc Natl Acad Sci U S A 107: 13707-13712.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 13707-13712
-
-
Frey, K.M.1
Georgiev, I.2
Donald, B.R.3
Anderson, A.C.4
-
4
-
-
79956017135
-
Computational design of proteins targeting the conserved stem region of influenza hemagglutinin
-
Fleishman SJ, Whitehead TA, Ekiert DC, Dreyfus C, Corn JE, et al. (2011) Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 332: 816-821.
-
(2011)
Science
, vol.332
, pp. 816-821
-
-
Fleishman, S.J.1
Whitehead, T.A.2
Ekiert, D.C.3
Dreyfus, C.4
Corn, J.E.5
-
5
-
-
0029366730
-
Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type-alpha transforming growth factor
-
Fadel AR, Jin DQ, Montelione GT, Levy RM, (1995) Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type-alpha transforming growth factor. J Biomol NMR 6: 221-226.
-
(1995)
J Biomol NMR
, vol.6
, pp. 221-226
-
-
Fadel, A.R.1
Jin, D.Q.2
Montelione, G.T.3
Levy, R.M.4
-
6
-
-
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.
-
(1998)
Science
, vol.282
, pp. 1462-1467
-
-
Harbury, P.B.1
Plecs, J.J.2
Tidor, B.3
Alber, T.4
Kim, P.S.5
-
7
-
-
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: 1099-1117.
-
(2007)
J Mol Biol
, vol.371
, pp. 1099-1117
-
-
Fu, X.1
Apgar, J.R.2
Keating, A.E.3
-
8
-
-
0345306764
-
Design of a novel globular protein fold with atomic-level accuracy
-
Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, et al. (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302: 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
-
9
-
-
32044456003
-
The backrub motion: how protein backbone shrugs when a sidechain dances
-
Davis IW, Arendall WB 3rd, Richardson DC, Richardson JS, (2006) The backrub motion: how protein backbone shrugs when a sidechain dances. Structure 14: 265-274.
-
(2006)
Structure
, vol.14
, pp. 265-274
-
-
Davis, I.W.1
Arendall 3rd, W.B.2
Richardson, D.C.3
Richardson, J.S.4
-
10
-
-
46249112114
-
Algorithm for backrub motions in protein design
-
Georgiev I, Keedy D, Richardson JS, Richardson DC, Donald BR, (2008) Algorithm for backrub motions in protein design. Bioinformatics 24: i196-204.
-
(2008)
Bioinformatics
, vol.24
-
-
Georgiev, I.1
Keedy, D.2
Richardson, J.S.3
Richardson, D.C.4
Donald, B.R.5
-
12
-
-
57049180165
-
Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design
-
Humphris EL, Kortemme T, (2008) Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design. Structure 16: 1777-1788.
-
(2008)
Structure
, vol.16
, pp. 1777-1788
-
-
Humphris, E.L.1
Kortemme, T.2
-
13
-
-
45649083705
-
A simple model of backbone flexibility improves modeling of side-chain conformational variability
-
Friedland GD, Linares AJ, Smith CA, Kortemme T, (2008) A simple model of backbone flexibility improves modeling of side-chain conformational variability. J Mol Biol 380: 757-774.
-
(2008)
J Mol Biol
, vol.380
, pp. 757-774
-
-
Friedland, G.D.1
Linares, A.J.2
Smith, C.A.3
Kortemme, T.4
-
14
-
-
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
-
15
-
-
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, C.3
Meiler, J.4
Kortemme, T.5
-
16
-
-
79960609097
-
Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design
-
Smith CA, Kortemme T, (2011) Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design. PLoS One 6: e20451.
-
(2011)
PLoS One
, vol.6
-
-
Smith, C.A.1
Kortemme, T.2
-
17
-
-
0024290472
-
Amino acid preferences for specific locations at the ends of alpha helices
-
Richardson JS, Richardson DC, (1988) Amino acid preferences for specific locations at the ends of alpha helices. Science 240: 1648-1652.
-
(1988)
Science
, vol.240
, pp. 1648-1652
-
-
Richardson, J.S.1
Richardson, D.C.2
-
18
-
-
0024290488
-
Helix signals in proteins
-
Presta LG, Rose GD, (1988) Helix signals in proteins. Science 240: 1632-1641.
-
(1988)
Science
, vol.240
, pp. 1632-1641
-
-
Presta, L.G.1
Rose, G.D.2
-
19
-
-
0024972479
-
Capping and alpha-helix stability
-
Serrano L, Fersht AR, (1989) Capping and alpha-helix stability. Nature 342: 296-299.
-
(1989)
Nature
, vol.342
, pp. 296-299
-
-
Serrano, L.1
Fersht, A.R.2
-
20
-
-
1842591839
-
Kinetic role of helix caps in protein folding is context-dependent
-
Kapp GT, Richardson JS, Oas TG, (2004) Kinetic role of helix caps in protein folding is context-dependent. Biochemistry 43: 3814-3823.
-
(2004)
Biochemistry
, vol.43
, pp. 3814-3823
-
-
Kapp, G.T.1
Richardson, J.S.2
Oas, T.G.3
-
21
-
-
0033229975
-
Experimental assessment of differences between related protein crystal structures
-
Kleywegt GJ, (1999) Experimental assessment of differences between related protein crystal structures. Acta Crystallogr D Biol Crystallogr 55: 1878-1884.
-
(1999)
Acta Crystallogr D Biol Crystallogr
, vol.55
, pp. 1878-1884
-
-
Kleywegt, G.J.1
-
22
-
-
0033166328
-
Errors and reproducibility in electron-density map interpretation
-
Mowbray SL, Helgstrand C, Sigrell JA, Cameron AD, Jones TA, (1999) Errors and reproducibility in electron-density map interpretation. Acta Crystallogr D Biol Crystallogr 55: 1309-1319.
-
(1999)
Acta Crystallogr D Biol Crystallogr
, vol.55
, pp. 1309-1319
-
-
Mowbray, S.L.1
Helgstrand, C.2
Sigrell, J.A.3
Cameron, A.D.4
Jones, T.A.5
-
23
-
-
0037441653
-
Structure validation by Calpha geometry: phi,psi and Cbeta deviation
-
Lovell SC, Davis IW, Arendall WB 3rd, de Bakker PI, Word JM, et al. (2003) Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins 50: 437-450.
-
(2003)
Proteins
, vol.50
, pp. 437-450
-
-
Lovell, S.C.1
Davis, I.W.2
Arendall 3rd, W.B.3
de Bakker, P.I.4
Word, J.M.5
-
24
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, et al. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117: 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
-
25
-
-
0033135638
-
Effective energy function for proteins in solution
-
Lazaridis T, Karplus M, (1999) Effective energy function for proteins in solution. Proteins 35: 133-152.
-
(1999)
Proteins
, vol.35
, pp. 133-152
-
-
Lazaridis, T.1
Karplus, M.2
-
26
-
-
84874028898
-
OSPREY: Protein Design with Ensembles, Flexibility, and Provable Algorithms
-
Gainza P, Roberts KE, Georgiev I, Lilien RH, Keedy DA, et al. (2012) OSPREY: Protein Design with Ensembles, Flexibility, and Provable Algorithms. Methods in Enzymology In press.
-
(2012)
Methods in Enzymology
-
-
Gainza, P.1
Roberts, K.E.2
Georgiev, I.3
Lilien, R.H.4
Keedy, D.A.5
-
27
-
-
0030010605
-
Experimentally observed conformation-dependent geometry and hidden strain in proteins
-
Karplus PA, (1996) Experimentally observed conformation-dependent geometry and hidden strain in proteins. Protein Sci 5: 1406-1420.
-
(1996)
Protein Sci
, vol.5
, pp. 1406-1420
-
-
Karplus, P.A.1
-
28
-
-
70349758444
-
Conformation dependence of backbone geometry in proteins
-
Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA, (2009) Conformation dependence of backbone geometry in proteins. Structure 17: 1316-1325.
-
(2009)
Structure
, vol.17
, pp. 1316-1325
-
-
Berkholz, D.S.1
Shapovalov, M.V.2
Dunbrack Jr., R.L.3
Karplus, P.A.4
-
29
-
-
0026619394
-
Looking at proteins: representations, folding, packing, and design. Biophysical Society National Lecture, 1992
-
Richardson JS, Richardson DC, Tweedy NB, Gernert KM, Quinn TP, et al. (1992) Looking at proteins: representations, folding, packing, and design. Biophysical Society National Lecture, 1992. Biophys J 63: 1185-1209.
-
(1992)
Biophys J
, vol.63
, pp. 1185-1209
-
-
Richardson, J.S.1
Richardson, D.C.2
Tweedy, N.B.3
Gernert, K.M.4
Quinn, T.P.5
-
30
-
-
0032424128
-
Aromatic rescue of glycine in beta sheets
-
Merkel JS, Regan L, (1998) Aromatic rescue of glycine in beta sheets. Fold Des 3: 449-455.
-
(1998)
Fold Des
, vol.3
, pp. 449-455
-
-
Merkel, J.S.1
Regan, L.2
-
31
-
-
0026320866
-
The energy landscapes and motions of proteins
-
Frauenfelder H, Sligar SG, Wolynes PG, (1991) The energy landscapes and motions of proteins. Science 254: 1598-1603.
-
(1991)
Science
, vol.254
, pp. 1598-1603
-
-
Frauenfelder, H.1
Sligar, S.G.2
Wolynes, P.G.3
-
32
-
-
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
-
33
-
-
34548040966
-
Crystal structure of an ancient protein: evolution by conformational epistasis
-
Ortlund EA, Bridgham JT, Redinbo MR, Thornton JW, (2007) Crystal structure of an ancient protein: evolution by conformational epistasis. Science 317: 1544-1548.
-
(2007)
Science
, vol.317
, pp. 1544-1548
-
-
Ortlund, E.A.1
Bridgham, J.T.2
Redinbo, M.R.3
Thornton, J.W.4
-
35
-
-
0037412183
-
Protein design is NP-hard
-
Pierce NA, Winfree E, (2002) Protein design is NP-hard. Protein Eng 15: 779-782.
-
(2002)
Protein Eng
, vol.15
, pp. 779-782
-
-
Pierce, N.A.1
Winfree, E.2
-
36
-
-
0033757806
-
The Protein Data Bank and the challenge of structural genomics
-
Berman HM, Bhat TN, Bourne PE, Feng Z, Gilliland G, et al. (2000) The Protein Data Bank and the challenge of structural genomics. Nat Struct Biol 7 Suppl: 957-959.
-
(2000)
Nat Struct Biol
, vol.7 Suppl
, pp. 957-959
-
-
Berman, H.M.1
Bhat, T.N.2
Bourne, P.E.3
Feng, Z.4
Gilliland, G.5
-
37
-
-
74549178560
-
MolProbity: all-atom structure validation for macromolecular crystallography
-
Chen VB, Arendall WB 3rd, Headd JJ, Keedy DA, Immormino RM, et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66: 12-21.
-
(2010)
Acta Crystallogr D Biol Crystallogr
, vol.66
, pp. 12-21
-
-
Chen, V.B.1
Arendall 3rd, W.B.2
Headd, J.J.3
Keedy, D.A.4
Immormino, R.M.5
-
38
-
-
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: 1735-1747.
-
(1999)
J Mol Biol
, vol.285
, pp. 1735-1747
-
-
Word, J.M.1
Lovell, S.C.2
Richardson, J.S.3
Richardson, D.C.4
-
39
-
-
70350509577
-
KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program
-
Chen VB, Davis IW, Richardson DC, (2009) KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program. Protein Sci 18: 2403-2409.
-
(2009)
Protein Sci
, vol.18
, pp. 2403-2409
-
-
Chen, V.B.1
Davis, I.W.2
Richardson, D.C.3
-
40
-
-
0026696173
-
Dissection of helix capping in T4 lysozyme by structural and thermodynamic analysis of six amino acid substitutions at Thr 59
-
Bell JA, Becktel WJ, Sauer U, Baase WA, Matthews BW, (1992) Dissection of helix capping in T4 lysozyme by structural and thermodynamic analysis of six amino acid substitutions at Thr 59. Biochemistry 31: 3590-3596.
-
(1992)
Biochemistry
, vol.31
, pp. 3590-3596
-
-
Bell, J.A.1
Becktel, W.J.2
Sauer, U.3
Baase, W.A.4
Matthews, B.W.5
-
41
-
-
0020997912
-
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C, (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
42
-
-
0033582329
-
Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering
-
Lovell SC, Word JM, Richardson JS, Richardson DC, (1999) Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering. Proc Natl Acad Sci U S A 96: 400-405.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 400-405
-
-
Lovell, S.C.1
Word, J.M.2
Richardson, J.S.3
Richardson, D.C.4
-
43
-
-
0034663722
-
The penultimate rotamer library
-
Lovell SC, Word JM, Richardson JS, Richardson DC, (2000) The penultimate rotamer library. Proteins 40: 389-408.
-
(2000)
Proteins
, vol.40
, pp. 389-408
-
-
Lovell, S.C.1
Word, J.M.2
Richardson, J.S.3
Richardson, D.C.4
-
44
-
-
0033613812
-
Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms
-
Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, et al. (1999) Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J Mol Biol 285: 1711-1733.
-
(1999)
J Mol Biol
, vol.285
, pp. 1711-1733
-
-
Word, J.M.1
Lovell, S.C.2
LaBean, T.H.3
Taylor, H.C.4
Zalis, M.E.5
|