-
1
-
-
79956017135
-
Computational design of proteins targeting the conserved stem region of influenza hemagglutinin
-
Fleishman, S.J. et al. Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 332, 816-821 (2011).
-
(2011)
Science
, vol.332
, pp. 816-821
-
-
Fleishman, S.J.1
-
2
-
-
77956338533
-
High-resolution mapping of protein sequence-function relationships
-
Fowler, D.M. et al. High-resolution mapping of protein sequence-function relationships. Nat. Methods 7, 741-746 (2010).
-
(2010)
Nat. Methods
, vol.7
, pp. 741-746
-
-
Fowler, D.M.1
-
3
-
-
80051794613
-
Deep mutational scanning: Assessing protein function on a massive scale
-
Araya, C.L. & Fowler, D.M. Deep mutational scanning: assessing protein function on a massive scale. Trends Biotechnol. 435-442 (2011).
-
(2011)
Trends Biotechnol.
, pp. 435-442
-
-
Araya, C.L.1
Fowler, D.M.2
-
4
-
-
34247176809
-
Isolating and engineering human antibodies using yeast surface display
-
Chao, G. et al. Isolating and engineering human antibodies using yeast surface display. Nat. Protoc. 1, 755-768 (2006).
-
(2006)
Nat. Protoc.
, vol.1
, pp. 755-768
-
-
Chao, G.1
-
5
-
-
0024403619
-
High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis
-
Cunningham, B.C. & Wells, J.A. High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis. Science 244, 1081-1085 (1989). (Pubitemid 19152300)
-
(1989)
Science
, vol.244
, Issue.4908
, pp. 1081-1085
-
-
Cunningham, B.C.1
Wells, J.A.2
-
6
-
-
0025363984
-
Deciphering the message in protein sequences: Tolerance to amino acid substitutions
-
Bowie, J.U., Reidhaar-Olson, J.F., Lim, W.A. & Sauer, R.T. Deciphering the message in protein sequences: tolerance to amino acid substitutions. Science 247, 1306-1310 (1990).
-
(1990)
Science
, vol.247
, pp. 1306-1310
-
-
Bowie, J.U.1
Reidhaar-Olson, J.F.2
Lim, W.A.3
Sauer, R.T.4
-
7
-
-
33746799726
-
Comprehensive and quantitative mapping of energy landscapes for protein-protein interactions by rapid combinatorial scanning
-
DOI 10.1074/jbc.M603826200
-
Pal, G., Kouadio, J.L., Artis, D.R., Kossiakoff, A.A. & Sidhu, S.S. Comprehensive and quantitative mapping of energy landscapes for protein-protein interactions by rapid combinatorial scanning. J. Biol. Chem. 281, 22378-22385 (2006). (Pubitemid 44181940)
-
(2006)
Journal of Biological Chemistry
, vol.281
, Issue.31
, pp. 22378-22385
-
-
Pal, G.1
Kouadio, J.-L.K.2
Artis, D.R.3
Kossiakoff, A.A.4
Sidhu, S.S.5
-
8
-
-
33845864966
-
Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein
-
DOI 10.1038/nature05385, PII NATURE05385
-
Bershtein, S., Segal, M., Bekerman, R., Tokuriki, N. & Tawfik, D.S. Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein. Nature 444, 929-932 (2006). (Pubitemid 46025005)
-
(2006)
Nature
, vol.444
, Issue.7121
, pp. 929-932
-
-
Bershtein, S.1
Segal, M.2
Bekerman, R.3
Tokuriki, N.4
Tawfik, D.S.5
-
9
-
-
79959615159
-
RosettaScripts: A scripting language interface to the rosetta macromolecular modeling suite
-
Fleishman, S.J. et al. RosettaScripts: a scripting language interface to the rosetta macromolecular modeling suite. PLoS ONE 6, e20161 (2011).
-
(2011)
PLoS ONE
, vol.6
-
-
Fleishman, S.J.1
-
10
-
-
78650905964
-
ROSETTA3: An object-oriented software suite for the simulation and design of macromolecules
-
Leaver-Fay, A. et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol. 487, 545-574 (2011).
-
(2011)
Methods Enzymol.
, vol.487
, pp. 545-574
-
-
Leaver-Fay, A.1
-
11
-
-
77952312935
-
Determinants of BH3 binding specificity for Mcl-1 versus Bcl-xL
-
Dutta, S. et al. Determinants of BH3 binding specificity for Mcl-1 versus Bcl-xL. J. Mol. Biol. 398, 747-762 (2010).
-
(2010)
J. Mol. Biol.
, vol.398
, pp. 747-762
-
-
Dutta, S.1
-
12
-
-
79952488320
-
Learning generative models for protein fold families
-
Balakrishnan, S., Kamisetty, H., Carbonell, J.G., Lee, S.I. & Langmead, C.J. Learning generative models for protein fold families. Proteins 79, 1061-1078 (2011).
-
(2011)
Proteins
, vol.79
, pp. 1061-1078
-
-
Balakrishnan, S.1
Kamisetty, H.2
Carbonell, J.G.3
Lee, S.I.4
Langmead, C.J.5
-
13
-
-
64849114224
-
Antibody recognition of a highly conserved influenza virus epitope
-
Ekiert, D.C. et al. Antibody recognition of a highly conserved influenza virus epitope. Science 324, 246-251 (2009).
-
(2009)
Science
, vol.324
, pp. 246-251
-
-
Ekiert, D.C.1
-
14
-
-
62049083943
-
Structural and functional bases for broad-spectrum neutralization of avian and human influenza A viruses
-
Sui, J. et al. Structural and functional bases for broad-spectrum neutralization of avian and human influenza A viruses. Nat. Struct. Mol. Biol. 16, 265-273 (2009).
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 265-273
-
-
Sui, J.1
-
15
-
-
79956357160
-
Experimental illumination of a fitness landscape
-
Hietpas, R.T., Jensen, J.D. & Bolon, D.N. Experimental illumination of a fitness landscape. Proc. Natl. Acad. Sci. USA 108, 7896-7901 (2011).
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 7896-7901
-
-
Hietpas, R.T.1
Jensen, J.D.2
Bolon, D.N.3
-
16
-
-
77957963240
-
Rapid construction of empirical RNA fitness landscapes
-
Pitt, J.N. & Ferre-D'Amare, A.R. Rapid construction of empirical RNA fitness landscapes. Science 330, 376-379 (2010).
-
(2010)
Science
, vol.330
, pp. 376-379
-
-
Pitt, J.N.1
Ferre-D'Amare, A.R.2
-
17
-
-
71849118573
-
High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis
-
Patwardhan, R.P. et al. High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nat. Biotechnol. 27, 1173-1175 (2009).
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 1173-1175
-
-
Patwardhan, R.P.1
-
18
-
-
77957357763
-
The fitness landscapes of cis-acting binding sites in different promoter and environmental contexts
-
Shultzaberger, R.K., Malashock, D.S., Kirsch, J.F. & Eisen, M.B. The fitness landscapes of cis-acting binding sites in different promoter and environmental contexts. PLoS Genet. 6, e1001042 (2010).
-
(2010)
PLoS Genet.
, vol.6
-
-
Shultzaberger, R.K.1
Malashock, D.S.2
Kirsch, J.F.3
Eisen, M.B.4
-
19
-
-
80052942203
-
Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing
-
Wu, X. et al. Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing. Science 333, 1593-1602 (2011).
-
(2011)
Science
, vol.333
, pp. 1593-1602
-
-
Wu, X.1
-
20
-
-
17744390877
-
Action-at-a-distance interactions enhance protein binding affinity
-
DOI 10.1110/ps.041283105
-
Joughin, B.A., Green, D.F. & Tidor, B. Action-at-a-distance interactions enhance protein binding affinity. Protein Sci. 14, 1363-1369 (2005). (Pubitemid 40577816)
-
(2005)
Protein Science
, vol.14
, Issue.5
, pp. 1363-1369
-
-
Joughin, B.A.1
Green, D.F.2
Tidor, B.3
-
21
-
-
17744382377
-
One- and two-body decomposable Poisson-Boltzmann methods for protein design calculations
-
DOI 10.1110/ps.041259105
-
Marshall, S.A., Vizcarra, C.L. & Mayo, S.L. One-and two-body decomposable Poisson-Boltzmann methods for protein design calculations. Protein Sci. 14, 1293-1304 (2005). (Pubitemid 40577809)
-
(2005)
Protein Science
, vol.14
, Issue.5
, pp. 1293-1304
-
-
Marshall, S.A.1
Vizcarra, C.L.2
Mayo, S.L.3
-
22
-
-
58049198443
-
Heterosubtypic neutralizing monoclonal antibodies cross-protective against H5N1 and H1N1 recovered from human IgM+ memory B cells
-
Throsby, M. et al. Heterosubtypic neutralizing monoclonal antibodies cross-protective against H5N1 and H1N1 recovered from human IgM+ memory B cells. PLoS ONE 3, e3942 (2008).
-
(2008)
PLoS ONE
, vol.3
-
-
Throsby, M.1
-
23
-
-
80051670323
-
A neutralizing antibody selected from plasma cells that binds to group 1 and group 2 influenza A hemagglutinins
-
Corti, D. et al. A neutralizing antibody selected from plasma cells that binds to group 1 and group 2 influenza A hemagglutinins. Science 333, 850-856 (2011).
-
(2011)
Science
, vol.333
, pp. 850-856
-
-
Corti, D.1
-
24
-
-
3242708140
-
Least angle regression
-
DOI 10.1214/009053604000000067
-
Efron, B., Hastie, T., Johnstone, I. & Tibshirani, R. Least angle regression. Ann. Stat. 32, 407-499 (2002). (Pubitemid 41250302)
-
(2004)
Annals of Statistics
, vol.32
, Issue.2
, pp. 407-499
-
-
Efron, B.1
Hastie, T.2
Johnstone, I.3
Tibshirani, R.4
Ishwaran, H.5
Knight, K.6
Loubes, J.-M.7
Massart, P.8
Madigan, D.9
Ridgeway, G.10
Rosset, S.11
Zhu, J.I.12
Stine, R.A.13
Turlach, B.A.14
Weisberg, S.15
Hastie, T.16
Johnstone, I.17
Tibshirani, R.18
-
25
-
-
77954656041
-
An improved yeast transformation method for the generation of very large human antibody libraries
-
Benatuil, L., Perez, J.M., Belk, J. & Hsieh, C.M. An improved yeast transformation method for the generation of very large human antibody libraries. Protein Eng. Des. Sel. 23, 155-159 (2010).
-
(2010)
Protein Eng. Des. Sel.
, vol.23
, pp. 155-159
-
-
Benatuil, L.1
Perez, J.M.2
Belk, J.3
Hsieh, C.M.4
-
26
-
-
14844294424
-
Protein production by auto-induction in high density shaking cultures
-
Studier, F.W. Protein production by auto-induction in high density shaking cultures. Protein Expr. Purif. 41, 207-234 (2005).
-
(2005)
Protein Expr. Purif.
, vol.41
, pp. 207-234
-
-
Studier, F.W.1
-
27
-
-
79551470095
-
Role of conformational sampling in computing mutation-induced changes in protein structure and stability
-
Kellogg, E.H., Leaver-Fay, A. & Baker, D. Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins 79, 830-838 (2011).
-
(2011)
Proteins
, vol.79
, pp. 830-838
-
-
Kellogg, E.H.1
Leaver-Fay, A.2
Baker, D.3
-
28
-
-
1642464839
-
Protein structure prediction using rosetta
-
DOI 10.1016/S0076-6879(04)83004-0
-
Rohl, C.A., Strauss, C.E., Misura, K.M. & Baker, D. Protein structure prediction using Rosetta. Methods Enzymol. 383, 66-93 (2004). (Pubitemid 38401787)
-
(2004)
Methods in Enzymology
, vol.383
, pp. 66-93
-
-
Rohl, C.A.1
Strauss, C.E.M.2
Misura, K.M.S.3
Baker, D.4
-
29
-
-
33748640631
-
Calculation of alkane to water solvation free energies using continuum solvent models
-
Sitkoff, D., BenTal, N. & Honig, B. Calculation of alkane to water solvation free energies using continuum solvent models. J. Phys. Chem. 100, 2744-2752 (1996). (Pubitemid 126793230)
-
(1996)
Journal of Physical Chemistry
, vol.100
, Issue.7
, pp. 2744-2752
-
-
Sitkoff, D.1
Ben-Tal, N.2
Honig, B.3
-
30
-
-
32844457567
-
Accurate calculation of hydration free-energies using macroscopic solvent models
-
Sitkoff, D., Sharp, K.A. & Honig, B. Accurate calculation of hydration free-energies using macroscopic solvent models. J. Phys. Chem. 98, 1978-1988 (1994).
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
31
-
-
0017429069
-
Areas volumes, packing, and protein-structure
-
Richards, F.M. Areas, volumes, packing, and protein-structure. Annu. Rev. Biophys. Bioeng. 6, 151-176 (1977).
-
(1977)
Annu. Rev. Biophys. Bioeng.
, vol.6
, pp. 151-176
-
-
Richards, F.M.1
-
32
-
-
34447508216
-
Phaser crystallographic software
-
DOI 10.1107/S0021889807021206, PII S0021889807021206
-
McCoy, A.J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674 (2007). (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
-
33
-
-
76449098262
-
PHENIX: A comprehensive Python-based system for macromolecular structure solution
-
Adams, P.D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213-221 (2010).
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 213-221
-
-
Adams, P.D.1
-
34
-
-
77949535720
-
Features and development of Coot
-
Emsley, P., Lohkamp, B., Scott, W.G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486-501 (2010).
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 486-501
-
-
Emsley, P.1
Lohkamp, B.2
Scott, W.G.3
Cowtan, K.4
-
35
-
-
33744459472
-
Toward the structural genomics of complexes: Crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis
-
DOI 10.1073/pnas.0602606103
-
Strong, M. et al. Toward the structural genomics of complexes: Crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 103, 8060-8065 (2006). (Pubitemid 43801052)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.21
, pp. 8060-8065
-
-
Strong, M.1
Sawaya, M.R.2
Wang, S.3
Phillips, M.4
Cascio, D.5
Eisenberg, D.6
-
36
-
-
0028304962
-
Satisfying hydrogen-bonding potential in proteins
-
McDonald, I.K. & Thornton, J.M. Satisfying hydrogen-bonding potential in proteins. J. Mol. Biol. 238, 777-793 (1994).
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 777-793
-
-
McDonald, I.K.1
Thornton, J.M.2
-
37
-
-
0023660979
-
Structure of myohemerythrin in the azidomet state at 1.7/1.3-Å resolution
-
Sheriff, S., Hendrickson, W.A. & Smith, J.L. Structure of myohemerythrin in the azidomet state at 1.7/1.3-Å resolution. J. Mol. Biol. 197, 273-296 (1987).
-
(1987)
J. Mol. Biol.
, vol.197
, pp. 273-296
-
-
Sheriff, S.1
Hendrickson, W.A.2
Smith, J.L.3
-
39
-
-
74549178560
-
MolProbity: All-atom structure validation for macromolecular crystallography
-
Chen, V.B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12-21 (2010).
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 12-21
-
-
Chen, V.B.1
-
40
-
-
70349331605
-
Triple combination of oseltamivir, amantadine, and ribavirin displays synergistic activity against multiple influenza virus strains in vitro
-
Nguyen, J.T. et al. Triple combination of oseltamivir, amantadine, and ribavirin displays synergistic activity against multiple influenza virus strains in vitro. Antimicrob. Agents Chemother. 53, 4115-4126 (2009).
-
(2009)
Antimicrob. Agents Chemother.
, vol.53
, pp. 4115-4126
-
-
Nguyen, J.T.1
-
41
-
-
0035115174
-
Cyclopentane neuraminidase inhibitors with potent in vitro anti-influenza virus activities
-
DOI 10.1128/AAC.45.3.743-748.2001
-
Smee, D.F., Huffman, J.H., Morrison, A.C., Barnard, D.L. & Sidwell, R.W. Cyclopentane neuraminidase inhibitors with potent in vitro anti-influenza virus activities. Antimicrob. Agents Chemother. 45, 743-748 (2001). (Pubitemid 32182019)
-
(2001)
Antimicrobial Agents and Chemotherapy
, vol.45
, Issue.3
, pp. 743-748
-
-
Smee, D.F.1
Huffman, J.H.2
Morrison, A.C.3
Barnard, D.L.4
Sidwell, R.W.5
-
42
-
-
77949639846
-
Triple combination of amantadine, ribavirin, and oseltamivir is highly active and synergistic against drug resistant influenza virus strains in vitro
-
Nguyen, J.T. et al. Triple combination of amantadine, ribavirin, and oseltamivir is highly active and synergistic against drug resistant influenza virus strains in vitro. PLoS ONE 5, e9332 (2010).
-
(2010)
PLoS ONE
, vol.5
-
-
Nguyen, J.T.1
-
43
-
-
4344589735
-
Fine epitope mapping of anti-epidermal growth factor receptor antibodies through random mutagenesis and yeast surface display
-
DOI 10.1016/j.jmb.2004.07.053, PII S0022283604008812
-
Chao, G., Cochran, J.R. & Wittrup, K.D. Fine epitope mapping of anti-epidermal growth factor receptor antibodies through random mutagenesis and yeast surface display. J. Mol. Biol. 342, 539-550 (2004). (Pubitemid 39149757)
-
(2004)
Journal of Molecular Biology
, vol.342
, Issue.2
, pp. 539-550
-
-
Chao, G.1
Cochran, J.R.2
Dane Wittrup, K.3
|