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12. Holm L, Sander C. Fast and simple Monte Carlo algorithm for side chain optimization in proteins: application
to model building by homology. Proteins: Struct Funct Genet . 1992;14:213
223.
13. Desmet J, Spriet J, Lasters I. Fast and accurate side-chain topology and energy refinement (FASTER) as a new
method for protein structure optimization. Proteins: Struct Funct Bioinf . 2002;48:31
43.
protein docking tested in blind predictions: the CAPRI experiment. Mol Biosyst .
14.
Janin J. Protein
2362.
15. Roberts KE, Cushing PR, Boisguerin P, Madden DR, Donald BR. Computational design of a PDZ domain
peptide inhibitor that rescues CFTR activity. PLoSComput Biol . 2012;8(4):e1002477.
16. Lippow SM, Wittrup KD, Tidor B. Computational design of antibody-affinity improvement beyond in vivo
maturation. Nat Biotechnol . 2007;25:1171
2010;6:2351
1176.
17. Haidar JN, Pierce B, Yu Y, Tong W, Li M, Weng Z. Structure-based design of a T-cell receptor leads to nearly
100-fold improvement in binding affinity for pepMHC. Proteins . 2009;74:948
960.
18. Leaver-Fay A, Jacak R, Stranges PB, Kuhlman B. A generic program for multistate protein design. PLoS ONE .
2011;6(7):e20937.
19. Kapp GT, Liu S, Stein A, et al. Control of protein signaling using a computationally designed GTPase/GEF
orthogonal pair. Proc Natl Acad Sci USA . 2012;109:5277 5282.
20. Grigoryan G, Reinke AW, Keating AE. Design of protein-interaction specificity gives selective bZIP-binding
peptides. Nature . 2009;458:859 864.
21. Yosef E, Politi R, Choi MH, Shifman JM. Computational design of calmodulin mutants with up to 900-fold
increase in binding specificity. J Mol Biol . 2009;385:1470 1480.
22. Karanicolas J, Kuhlman B. Computational design of affinity and specificity at protein protein interfaces. Curr
Opin Struct Biol . 2009;19:458
463.
23. Fleishman SJ, Corn JE, Strauch E-M, Whitehead TA, Karanicolas J, Baker D. Hotspot-centric de novo design of
protein binders. J Mol Biol . 2011;413:1047
1062.
24. Fleishman SJ, Whitehead TA, Ekiert DC, et al. Computational design of proteins targeting the conserved stem
region of influenza hemagglutinin. Science . 2011;332:816
821.
25. Bogan AA, Thorn KS. Anatomy of hot spots in protein interfaces. J Mol Biol . 1998;280:1
9.
26. Davis IW, Baker D. RosettaLigand docking with full ligand and receptor flexibility. J Mol Biol .
2009;385:381
392.
121
27.
Jha RK, Leaver-Fay A, Yin S, et al. Computational design of a PAK1 binding protein. J Mol Biol .
2010;400:257
270.
28. Stranges PB, Machius M, Miley MJ, et al. Computational design of a symmetric homodimer using
β
-strand
20567.
29. Der BS, Machius M, Miley MJ, Mills JL, Szyperski T, Kuhlman B. Metal-mediated affinity and
orientation specificity in a computationally designed protein homodimer. JAmChemSoc .
2012;134:375 385.
30. Salgado EN, Ambroggio XI, Brodin JD, Lewis RA, Kuhlman B, Tezcan FA. Metal templated design of protein
interfaces. Proc Natl Acad Sci USA . 2010;107:1827 1832.
31. Sia SK, Kim PS. Protein grafting of an HIV-1-inhibiting epitope. Proc Natl Acad Sci USA . 2003;100:9756 9761.
32. Azoitei ML, Correia BE, Ban Y-EA, et al. Computation-guided backbone grafting of a discontinuous motif onto
a protein scaffold. Science . 2011;334:373 376.
33. Garcia-Viloca M, Gao J, Karplus M, Truhlar DG. How enzymes work: analysis by modern rate theory and
computer simulations. Science . 2004;303:186 195.
34. Bhabha G, Lee J, Ekiert DC, et al. A dynamic knockout reveals that conformational fluctuations influence the
chemical step of enzyme catalysis. Science . 2011;332:234
assembly. Proc Natl Acad Sci USA . 2011;108:20562
238.
35. Richter F, Leaver-Fay A, Khare SD, Bjelic S, Baker D. De novo enzyme design using rosetta3. PLoS ONE .
2011;6(5):e19230.
36. Chen C-Y, Georgiev I, Anderson AC, Donald BR. Computational structure-based redesign of enzyme activity.
Proc Natl Acad Sci USA . 2009;106:3764
3769.
37. Ashworth J, Havranek JJ, Duarte CM, et al. Computational redesign of endonuclease DNA binding and
cleavage specificity. Nature . 2006;441:656
659.
38. Gao H, Smith J, Yang M, et al. Heritable targeted mutagenesis in maize using a designed endonuclease. Plant J .
2010;61:176
187.
39. Windbichler N, Menichelli M, Papathanos PA, et al. A synthetic homing endonuclease-based gene drive system
in the human malaria mosquito. Nature . 2011;473:212
215.
40. Murphy PM, Bolduc JM, Gallaher JL, Stoddard BL, Baker D. Alteration of enzyme specificity by computational
loop remodeling and design. Proc Natl Acad Sci USA . 2009;106:9215
9220.
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