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Volumn 99, Issue 10, 2010, Pages 3445-3453

Discovery of entry inhibitors for HIV-1 via a new de novo protein design framework

Author keywords

[No Author keywords available]

Indexed keywords

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 78649244595     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.09.050     Document Type: Article
Times cited : (38)

References (73)
  • 2
    • 53549110515 scopus 로고    scopus 로고
    • Resetting priorities
    • Thayer, A. M. 2008. Resetting priorities. Chem. Eng. News. 86:17-28.
    • (2008) Chem. Eng. News. , vol.86 , pp. 17-28
    • Thayer, A.M.1
  • 3
    • 53549126978 scopus 로고    scopus 로고
    • New antiretrovirals
    • Thayer, A. M. 2008. New antiretrovirals. Chem. Eng. News. 86:29-36.
    • (2008) Chem. Eng. News. , vol.86 , pp. 29-36
    • Thayer, A.M.1
  • 4
    • 0032577550 scopus 로고    scopus 로고
    • HIV entry and its inhibition
    • Chan, D. C., and P. S. Kim. 1998. HIV entry and its inhibition. Cell. 93:681-684.
    • (1998) Cell. , vol.93 , pp. 681-684
    • Chan, D.C.1    Kim, P.S.2
  • 5
    • 33846173312 scopus 로고    scopus 로고
    • HIVentry inhibitors targeting gp41: From polypeptides to small-molecule compounds
    • Liu, S.W., S. G.Wu, and S. B. Jiang. 2007. HIVentry inhibitors targeting gp41: from polypeptides to small-molecule compounds. Curr. Pharm. Des. 13:143-162.
    • (2007) Curr. Pharm. Des. , vol.13 , pp. 143-162
    • Liu, S.W.1    Wu, S.G.2    Jiang, S.B.3
  • 6
    • 57649155175 scopus 로고    scopus 로고
    • Rationally designed anti-HIV peptides containing multifunctional domains as molecule probes for studying the mechanisms of action of the first and second generation HIV fusion inhibitors
    • Qi, Z., W. G. Shi, ., S. Jiang. 2008. Rationally designed anti-HIV peptides containing multifunctional domains as molecule probes for studying the mechanisms of action of the first and second generation HIV fusion inhibitors. J. Biol. Chem. 283:30376-30384.
    • (2008) J. Biol. Chem. , vol.283 , pp. 30376-30384
    • Qi, Z.1    Shi, W.G.2    Jiang, S.3
  • 7
    • 46049096485 scopus 로고    scopus 로고
    • Dose-response curve slope sets class-specific limits on inhibitory potential of anti-HIV drugs
    • Shen, L., S. Peterson, ., R. F. Siliciano. 2008. Dose-response curve slope sets class-specific limits on inhibitory potential of anti-HIV drugs. Nat. Med. 14:762-766.
    • (2008) Nat. Med. , vol.14 , pp. 762-766
    • Shen, L.1    Peterson, S.2    Siliciano, R.F.3
  • 8
    • 27644510382 scopus 로고    scopus 로고
    • Maraviroc (UK-427,857), a potent, orally bioavailable, and selective small-molecule inhibitor of chemokine receptor CCR5 with broad-spectrum anti-human immunodeficiency virus type 1 activity
    • Dorr, P., M. Westby, ., M. Perros. 2005. Maraviroc (UK-427,857), a potent, orally bioavailable, and selective small-molecule inhibitor of chemokine receptor CCR5 with broad-spectrum anti-human immunodeficiency virus type 1 activity. Antimicrob. Agents Chemother. 49:4721-4732.
    • (2005) Antimicrob. Agents Chemother. , vol.49 , pp. 4721-4732
    • Dorr, P.1    Westby, M.2    Perros, M.3
  • 10
    • 0037069386 scopus 로고    scopus 로고
    • Short constrained peptides that inhibit HIV-1 entry
    • Sia, S. K., P. A. Carr, ., P. S. Kim. 2002. Short constrained peptides that inhibit HIV-1 entry. Proc. Natl. Acad. Sci. USA. 99:14664-14669.
    • (2002) Proc. Natl. Acad. Sci. USA. , vol.99 , pp. 14664-14669
    • Sia, S.K.1    Carr, P.A.2    Kim, P.S.3
  • 11
    • 64149109197 scopus 로고    scopus 로고
    • Design of peptidebased inhibitors for human immunodeficiency virus type 1 strains resistant to T-20
    • Izumi, K., E. Kodama, ., M. Matsuoka. 2009. Design of peptidebased inhibitors for human immunodeficiency virus type 1 strains resistant to T-20. J. Biol. Chem. 284:4914-4920.
    • (2009) J. Biol. Chem. , vol.284 , pp. 4914-4920
    • Izumi, K.1    Kodama, E.2    Matsuoka, M.3
  • 12
    • 62949102876 scopus 로고    scopus 로고
    • SC29EK, a peptide fusion inhibitor with enhanced a-helicity, inhibits replication of human immunodeficiency virus type 1 mutants resistant to Enfuvirtide
    • Naito, T., K. Izumi,., M. Matsuoka. 2009. SC29EK, a peptide fusion inhibitor with enhanced a-helicity, inhibits replication of human immunodeficiency virus type 1 mutants resistant to Enfuvirtide. Antimicrob. Agents Chemother. 53:1013-1018.
    • (2009) Antimicrob. Agents Chemother. , vol.53 , pp. 1013-1018
    • Naito, T.1    Izumi., K.2    Matsuoka, M.3
  • 13
    • 59649099932 scopus 로고    scopus 로고
    • Electrostatically constrained α-helical peptide inhibits replication of HIV-1 resistant to Enfuvirtide
    • Nishikawa, H., S. Nakamura,., M. Matsuoka. 2009. Electrostatically constrained α-helical peptide inhibits replication of HIV-1 resistant to Enfuvirtide. Int. J. Biochem. Cell Biol. 41:891-899.
    • (2009) Int. J. Biochem. Cell Biol. , vol.41 , pp. 891-899
    • Nishikawa, H.1    Nakamura., S.2    Matsuoka, M.3
  • 14
    • 34547854349 scopus 로고    scopus 로고
    • Design of helical, oligomeric HIV-1 fusion inhibitor peptides with potent activity against Enfuvirtide-resistant virus
    • Dwyer, J. J., K. L. Wilson, ., M. K. Delmedico. 2007. Design of helical, oligomeric HIV-1 fusion inhibitor peptides with potent activity against Enfuvirtide-resistant virus. Proc. Natl. Acad. Sci. USA. 104:12772-12777.
    • (2007) Proc. Natl. Acad. Sci. USA. , vol.104 , pp. 12772-12777
    • Dwyer, J.J.1    Wilson, K.L.2    Delmedico, M.K.3
  • 15
    • 45549093277 scopus 로고    scopus 로고
    • Design and evaluation of Sifuvirtide, a novel HIV-1 fusion inhibitor
    • He, Y., Y. Xiao, ., L. Zhang. 2008. Design and evaluation of Sifuvirtide, a novel HIV-1 fusion inhibitor. J. Biol. Chem. 283:11126-11134.
    • (2008) J. Biol. Chem. , vol.283 , pp. 11126-11134
    • He, Y.1    Xiao, Y.2    Zhang, L.3
  • 16
    • 68049108497 scopus 로고    scopus 로고
    • NMR second site screening for structure determination of ligands bound in the hydrophobic pocket of HIV-1 gp41
    • Balogh, E., D. Wu, ., M. Gochin. 2009. NMR second site screening for structure determination of ligands bound in the hydrophobic pocket of HIV-1 gp41. J. Am. Chem. Soc. 131:2821-2823.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 2821-2823
    • Balogh, E.1    Wu, D.2    Gochin, M.3
  • 17
    • 37349002730 scopus 로고    scopus 로고
    • Design and synthesis of human immunodeficiency virus entry inhibitors: Sulfonamide as an isostere for the α-ketoamide group
    • Lu, R. J., J. A. Tucker, ., C. Sexton. 2007. Design and synthesis of human immunodeficiency virus entry inhibitors: sulfonamide as an isostere for the α-ketoamide group. J. Med. Chem. 50:6535-6544.
    • (2007) J. Med. Chem. , vol.50 , pp. 6535-6544
    • Lu, R.J.1    Tucker, J.A.2    Sexton, C.3
  • 18
    • 61949186713 scopus 로고    scopus 로고
    • Comparative docking study of anibamine as the first natural product CCR5 antagonist in CCR5 homology models
    • Li, G., K. M. Haney,., Y. Zhang. 2009. Comparative docking study of anibamine as the first natural product CCR5 antagonist in CCR5 homology models. J. Chem. Inf. Model. 49:120-132.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 120-132
    • Li, G.1    Haney., K.M.2    Zhang, Y.3
  • 19
    • 55249083812 scopus 로고    scopus 로고
    • Small-molecule CD4 mimics interact with a highly conserved pocket on HIV-1 gp120
    • Madani, N., A. Schön, ., J. Sodroski. 2008. Small-molecule CD4 mimics interact with a highly conserved pocket on HIV-1 gp120. Structure. 16:1689-1701.
    • (2008) Structure. , vol.16 , pp. 1689-1701
    • Madani, N.1    Schön, A.2    Sodroski, J.3
  • 20
    • 58149090406 scopus 로고    scopus 로고
    • Design, synthesis, and biological evaluation of N-carboxyphenylpyrrole derivatives as potent HIV fusion inhibitors targeting gp41
    • Liu, K., H. Lu,., L. Xie. 2008. Design, synthesis, and biological evaluation of N-carboxyphenylpyrrole derivatives as potent HIV fusion inhibitors targeting gp41. J. Med. Chem. 51:7843-7854.
    • (2008) J. Med. Chem. , vol.51 , pp. 7843-7854
    • Liu, K.1    Lu, H.2    Xie, L.3
  • 21
    • 75749112873 scopus 로고    scopus 로고
    • Manipulation of electrostatic and saccharide linker interactions in the design of efficient glycopolypeptide-based cholera toxin inhibitors
    • Maheshwari, R., E. A. Levenson, and K. L. Kiick. 2010. Manipulation of electrostatic and saccharide linker interactions in the design of efficient glycopolypeptide-based cholera toxin inhibitors. Macromol. Biosci. 10:68-81.
    • (2010) Macromol. Biosci. , vol.10 , pp. 68-81
    • Maheshwari, R.1    Levenson, E.A.2    Kiick, K.L.3
  • 22
    • 65249085618 scopus 로고    scopus 로고
    • Addition of a cholesterol group to an HIV-1 peptide fusion inhibitor dramatically increases its antiviral potency
    • Ingallinella, P., E. Bianchi,., A. Pessi. 2009. Addition of a cholesterol group to an HIV-1 peptide fusion inhibitor dramatically increases its antiviral potency. Proc. Natl. Acad. Sci. USA. 106:5801-5806.
    • (2009) Proc. Natl. Acad. Sci. USA. , vol.106 , pp. 5801-5806
    • Ingallinella, P.1    Bianchi., E.2    Pessi, A.3
  • 23
    • 59149094807 scopus 로고    scopus 로고
    • Computer-based design of novel HIV-1 entry inhibitors: Neomycin conjugated to arginine peptides at two specific sites
    • Berchanski, A., and A. Lapidot. 2009. Computer-based design of novel HIV-1 entry inhibitors: neomycin conjugated to arginine peptides at two specific sites. J. Mol. Model. 15:281-294.
    • (2009) J. Mol. Model. , vol.15 , pp. 281-294
    • Berchanski, A.1    Lapidot, A.2
  • 24
    • 33846147981 scopus 로고    scopus 로고
    • Inhibition of HIV-1 infection by synthetic peptides derived CCR5 fragments
    • Imai, M., L. Baranyi,., H. Okada. 2007. Inhibition of HIV-1 infection by synthetic peptides derived CCR5 fragments. Biochem. Biophys. Res. Commun. 353:851-856.
    • (2007) Biochem. Biophys. Res. Commun. , vol.353 , pp. 851-856
    • Imai, M.1    Baranyi., L.2    Okada, H.3
  • 25
    • 40449101942 scopus 로고    scopus 로고
    • Computational de novo peptide and protein design: Rigid templates versus flexible templates
    • Fung, H. K., W. J. Welsh, and C. A. Floudas. 2008. Computational de novo peptide and protein design: rigid templates versus flexible templates. Ind. Eng. Chem. Res. 47:993-1001.
    • (2008) Ind. Eng. Chem. Res. , vol.47 , pp. 993-1001
    • Fung, H.K.1    Welsh, W.J.2    Floudas, C.A.3
  • 26
    • 27844505722 scopus 로고    scopus 로고
    • Advances in protein structure prediction and de novo protein design: A review
    • Floudas, C. A., H. K. Fung,., R. Rajgaria. 2006. Advances in protein structure prediction and de novo protein design: a review. Chem. Eng. Sci. 61:966-988.
    • (2006) Chem. Eng. Sci. , vol.61 , pp. 966-988
    • Floudas, C.A.1    Fung., H.K.2    Rajgaria, R.3
  • 27
    • 1042298843 scopus 로고    scopus 로고
    • Computational design of proteinprotein interactions
    • Kortemme, T., and D. Baker. 2004. Computational design of proteinprotein interactions. Curr. Opin. Chem. Biol. 8:91-97.
    • (2004) Curr. Opin. Chem. Biol. , vol.8 , pp. 91-97
    • Kortemme, T.1    Baker, D.2
  • 28
    • 1342324030 scopus 로고    scopus 로고
    • Exploring folding free energy landscapes using computational protein design
    • Kuhlman, B., and D. Baker. 2004. Exploring folding free energy landscapes using computational protein design. Curr. Opin. Struct. Biol. 14:89-95.
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 89-95
    • Kuhlman, B.1    Baker, D.2
  • 29
    • 0026589733 scopus 로고
    • The dead-end elimination theorem and its use in side-chain positioning
    • Desmet, J., M. D. Maeyer, ., I. Lasters. 1992. The dead-end elimination theorem and its use in side-chain positioning. Nature. 356: 539-542.
    • (1992) Nature. , vol.356 , pp. 539-542
    • Desmet, J.1    Maeyer, M.D.2    Lasters, I.3
  • 30
    • 0001114311 scopus 로고    scopus 로고
    • Conformational splitting: A more powerful criterion for dead-end elimination
    • Pierce, N., J. Spriet, ., S. Mayo. 2000. Conformational splitting: a more powerful criterion for dead-end elimination. J. Comput. Chem. 21:999-1009.
    • (2000) J. Comput. Chem. , vol.21 , pp. 999-1009
    • Pierce, N.1    Spriet, J.2    Mayo, S.3
  • 31
    • 34547840252 scopus 로고    scopus 로고
    • Dead-end elimination with backbone flexibility
    • Georgiev, I., and B. R. Donald. 2007. Dead-end elimination with backbone flexibility. Bioinformatics. 23:i185-i194.
    • (2007) Bioinformatics. , vol.23
    • Georgiev, I.1    Donald, B.R.2
  • 32
    • 0028343413 scopus 로고
    • Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy
    • Koehl, P., and M. Delarue. 1994. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J. Mol. Biol. 239:249-275.
    • (1994) J. Mol. Biol. , vol.239 , pp. 249-275
    • Koehl, P.1    Delarue, M.2
  • 33
    • 0036667734 scopus 로고    scopus 로고
    • Combinatorial protein design
    • Saven, J. G. 2002. Combinatorial protein design. Curr. Opin. Struct. Biol. 12:453-458.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 453-458
    • Saven, J.G.1
  • 34
    • 0037460608 scopus 로고    scopus 로고
    • Using self-consistent fields to bias Monte Carlo methods with applications to designing and sampling protein sequences
    • Zou, J. M., and J. G. Saven. 2003. Using self-consistent fields to bias Monte Carlo methods with applications to designing and sampling protein sequences. J. Chem. Phys. 118:3843-3854.
    • (2003) J. Chem. Phys. , vol.118 , pp. 3843-3854
    • Zou, J.M.1    Saven, J.G.2
  • 35
    • 0033550206 scopus 로고    scopus 로고
    • De novo protein design. I. in search of stability and specificity
    • Koehl, P., and M. Levitt. 1999. De novo protein design. I. In search of stability and specificity. J. Mol. Biol. 293:1161-1181.
    • (1999) J. Mol. Biol. , vol.293 , pp. 1161-1181
    • Koehl, P.1    Levitt, M.2
  • 36
    • 0033550264 scopus 로고    scopus 로고
    • De novo protein design. II. Plasticity in sequence space
    • Koehl, P., and M. Levitt. 1999. De novo protein design. II. Plasticity in sequence space. J. Mol. Biol. 293:1183-1193.
    • (1999) J. Mol. Biol. , vol.293 , pp. 1183-1193
    • Koehl, P.1    Levitt, M.2
  • 37
    • 0041387567 scopus 로고    scopus 로고
    • A large scale test of computational protein design: Folding and stability of nine completely redesigned globular proteins
    • Baker
    • Dantas, G., B. Kuhlman, ., D. Baker. 2003. A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. J. Mol. Biol. 332:449-460.
    • (2003) J. Mol. Biol. , vol.332 , pp. 449-460
    • Dantas, G.1    Kuhlman . D, B.2
  • 38
    • 0030762021 scopus 로고    scopus 로고
    • Coupling backbone flexibility and amino acid sequence selection in protein design
    • Su, A., and S. L. Mayo. 1997. Coupling backbone flexibility and amino acid sequence selection in protein design. Protein Sci. 6:1701-1707.
    • (1997) Protein Sci. , vol.6 , pp. 1701-1707
    • Su, A.1    Mayo, S.L.2
  • 39
    • 12544260150 scopus 로고    scopus 로고
    • Recapitulation of protein family divergence using flexible backbone protein design
    • Saunders, C. T., and D. Baker. 2005. Recapitulation of protein family divergence using flexible backbone protein design. J. Mol. Biol. 346:631-644.
    • (2005) J. Mol. Biol. , vol.346 , pp. 631-644
    • Saunders, C.T.1    Baker, D.2
  • 40
    • 33845292929 scopus 로고    scopus 로고
    • Novel formulations for the sequence selection problem in de novo protein design with flexible templates
    • Fung, H. K., M. S. Taylor, and C. A. Floudas. 2007. Novel formulations for the sequence selection problem in de novo protein design with flexible templates. Optimiz. Meth. Softw. 22:51-71.
    • (2007) Optimiz. Meth. Softw. , vol.22 , pp. 51-71
    • Fung, H.K.1    Taylor, M.S.2    Floudas, C.A.3
  • 41
    • 0035862545 scopus 로고    scopus 로고
    • N- and C-domains of HIV- 1 gp41: Mutation, structure and functions
    • Dong, X.-N., Y. Xiao,., Y. H. Chen. 2001. N- and C-domains of HIV- 1 gp41: mutation, structure and functions. Immunol. Lett. 75:215-220.
    • (2001) Immunol. Lett. , vol.75 , pp. 215-220
    • Dong, X.-N.1    Xiao., Y.2    Chen, Y.H.3
  • 42
    • 0033214895 scopus 로고    scopus 로고
    • Inhibiting HIV- 1 entry: Discovery of D-peptide inhibitors that target the gp41 coiledcoil pocket
    • Eckert, D. M., V. N. Malashkevich,., P. S. Kim. 1999. Inhibiting HIV- 1 entry: discovery of D-peptide inhibitors that target the gp41 coiledcoil pocket. Cell. 99:103-115.
    • (1999) Cell. , vol.99 , pp. 103-115
    • Eckert, D.M.1    Malashkevich., V.N.2    Kim, P.S.3
  • 43
    • 0032433685 scopus 로고    scopus 로고
    • Evidence that a prominent cavity in the coiled coil of HIV type 1 gp41 is an attractive drug target
    • Chan, D. C., C. T. Chutkowski, and P. S. Kim. 1998. Evidence that a prominent cavity in the coiled coil of HIV type 1 gp41 is an attractive drug target. Proc. Natl. Acad. Sci. USA. 95:15613-15617.
    • (1998) Proc. Natl. Acad. Sci. USA. , vol.95 , pp. 15613-15617
    • Chan, D.C.1    Chutkowski, C.T.2    Kim, P.S.3
  • 44
    • 0030970693 scopus 로고    scopus 로고
    • Core structure of gp41 from the HIV envelope glycoprotein
    • Chan, D. C., D. Fass,., P. S. Kim. 1997. Core structure of gp41 from the HIV envelope glycoprotein. Cell. 89:263-273.
    • (1997) Cell. , vol.89 , pp. 263-273
    • Chan, D.C.1    Fass., D.2    Kim, P.S.3
  • 45
    • 38349008761 scopus 로고    scopus 로고
    • Toward full-sequence de novo protein design with flexible templates for human b-defensin-2
    • Fung, H. K., C. A. Floudas,., D. Morikis. 2008. Toward full-sequence de novo protein design with flexible templates for human b-defensin-2. Biophys. J. 94:584-599.
    • (2008) Biophys. J. , vol.94 , pp. 584-599
    • Fung, H.K.1    Floudas., C.A.2    Morikis, D.3
  • 46
    • 33750050261 scopus 로고    scopus 로고
    • A novel high resolution Ca-Ca distance dependent force field based on a high quality decoy set
    • Rajgaria, R., S. R. McAllister, and C. A. Floudas. 2006. A novel high resolution Ca-Ca distance dependent force field based on a high quality decoy set. Proteins: Struct. Funct. Bioinf. 65:726-741.
    • (2006) Proteins: Struct. Funct. Bioinf. , vol.65 , pp. 726-741
    • Rajgaria, R.1    McAllister, S.R.2    Floudas, C.A.3
  • 47
    • 38549146473 scopus 로고    scopus 로고
    • Distance dependent centroid to centroid force fields using high resolution decoys
    • Rajgaria, R., S. R. McAllister, and C. A. Floudas. 2008. Distance dependent centroid to centroid force fields using high resolution decoys. Proteins. 70:950-970.
    • (2008) Proteins. , vol.70 , pp. 950-970
    • Rajgaria, R.1    McAllister, S.R.2    Floudas, C.A.3
  • 48
    • 0346458791 scopus 로고    scopus 로고
    • A new pairwise folding potential based on improved decoy generation and side chain packing
    • Loose, C., J. Klepeis, and C. Floudas. 2004. A new pairwise folding potential based on improved decoy generation and side chain packing. Proteins: Struct. Funct. Bioinf. 54:303-314.
    • (2004) Proteins: Struct. Funct. Bioinf. , vol.54 , pp. 303-314
    • Loose, C.1    Klepeis, J.2    Floudas, C.3
  • 49
    • 0037699589 scopus 로고    scopus 로고
    • Integrated computational and experimental approach for lead optimization and design of compstatin variants with improved activity
    • Klepeis, J. L., C. A. Floudas, ., J. D. Lambris. 2003. Integrated computational and experimental approach for lead optimization and design of compstatin variants with improved activity. J. Am. Chem. Soc. 125:8422-8423.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 8422-8423
    • Klepeis, J.L.1    Floudas, C.A.2    Lambris, J.D.3
  • 50
    • 3042785531 scopus 로고    scopus 로고
    • Design of peptide analogs with improved activity using a novel de novo protein design approach
    • Klepeis, J. L., C. A. Floudas,., J. D. Lambris. 2004. Design of peptide analogs with improved activity using a novel de novo protein design approach. Ind. Eng. Chem. Res. 43:3817-3826.
    • (2004) Ind. Eng. Chem. Res. , vol.43 , pp. 3817-3826
    • Klepeis, J.L.1    Floudas., C.A.2    Lambris, J.D.3
  • 51
    • 0141642142 scopus 로고    scopus 로고
    • ASTRO-FOLD: A combinatorial and global optimization framework for ab initio prediction of threedimensional structures of proteins from the amino acid sequence
    • Klepeis, J. L., and C. A. Floudas. 2003. ASTRO-FOLD: A combinatorial and global optimization framework for ab initio prediction of threedimensional structures of proteins from the amino acid sequence. Biophys. J. 85:2119-2146.
    • (2003) Biophys. J. , vol.85 , pp. 2119-2146
    • Klepeis, J.L.1    Floudas, C.A.2
  • 52
    • 0000292903 scopus 로고    scopus 로고
    • Predicting peptide structures using NMR data and deterministic global optimization
    • Klepeis, J. L., C. A. Floudas, D. Morikis, and J. D. Lambris. 1999. Predicting peptide structures using NMR data and deterministic global optimization. J. Comput. Chem. 20:1354-1370.
    • (1999) J. Comput. Chem. , vol.20 , pp. 1354-1370
    • Klepeis, J.L.1    Floudas, C.A.2    Morikis, D.3    Lambris, J.D.4
  • 53
    • 0000812896 scopus 로고    scopus 로고
    • Free energy calculations for peptides via deterministic global optimization
    • Klepeis, J. L., and C. A. Floudas. 1999. Free energy calculations for peptides via deterministic global optimization. J. Chem. Phys. 110: 7491-7512.
    • (1999) J. Chem. Phys. , vol.110 , pp. 7491-7512
    • Klepeis, J.L.1    Floudas, C.A.2
  • 54
    • 34249824268 scopus 로고    scopus 로고
    • Computational methods in protein structure prediction
    • Floudas, C. A. 2007. Computational methods in protein structure prediction. Biotechnol. and Bioeng. 97:207-213.
    • (2007) Biotechnol. and Bioeng. , vol.97 , pp. 207-213
    • Floudas, C.A.1
  • 55
    • 0031576336 scopus 로고    scopus 로고
    • Torsion angle dynamics for NMR structure calculation with the new program DYANA
    • Güntert, P., C. Mumenthaler, and K. Wüthrich. 1997. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273:283-298.
    • (1997) J. Mol. Biol. , vol.273 , pp. 283-298
    • Güntert, P.1    Mumenthaler, C.2    Wüthrich, K.3
  • 56
    • 4644340524 scopus 로고    scopus 로고
    • Automated NMR structure calculation with CYANA
    • Guntert, P. 2004. Automated NMR structure calculation with CYANA. Meth. Mol. Biol. J. Mol. Biol. 278:353-378.
    • (2004) Meth. Mol. Biol. J. Mol. Biol. , vol.278 , pp. 353-378
    • Guntert, P.1
  • 57
    • 0003684555 scopus 로고    scopus 로고
    • Department of Biochemistry and Molecular Biophysics. Washington University School of Medicine, St. Louis, MO
    • Ponder, J. 1998. TINKER, software tools for molecular design. Department of Biochemistry and Molecular Biophysics. Washington University School of Medicine, St. Louis, MO.
    • (1998) TINKER, Software Tools for Molecular Design
    • Ponder, J.1
  • 58
    • 0029011701 scopus 로고
    • A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organicmolecules
    • Cornell, W. D., P. Cieplak, ., P. A. Kollman. 1995. A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organicmolecules. J. Am. Chem. Soc. 117:5179-5197.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 5179-5197
    • Cornell, W.D.1    Cieplak, P.2    Kollman, P.A.3
  • 59
    • 77950810925 scopus 로고    scopus 로고
    • New compstatin variants through two de novo protein design frameworks
    • Bellows, M. L., H. K. Fung, ., D. Morikis. 2010. New compstatin variants through two de novo protein design frameworks. Biophys. J. 98:2337-2346.
    • (2010) Biophys. J. , vol.98 , pp. 2337-2346
    • Bellows, M.L.1    Fung, H.K.2    Morikis., D.3
  • 60
    • 23844557146 scopus 로고    scopus 로고
    • A novel ensemble-based scoring and search algorithm for protein redesign and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme
    • Lilien, R. H., B. W. Stevens, ., B. R. Donald. 2005. A novel ensemble-based scoring and search algorithm for protein redesign and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme. J. Comput. Biol. 12:740-761.
    • (2005) J. Comput. Biol. , vol.12 , pp. 740-761
    • Lilien, R.H.1    Stevens, B.W.2    Donald, B.R.3
  • 61
    • 0035857402 scopus 로고    scopus 로고
    • 2.1 and 1.8Å average C (a) RMSD structure predictions on two small proteins, HP-36 and s15
    • Lee, M. R., D. Baker, and P. A. Kollman. 2001. 2.1 and 1.8Å average C (a) RMSD structure predictions on two small proteins, HP-36 and s15. J. Am. Chem. Soc. 123:1040-1046.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 1040-1046
    • Lee, M.R.1    Baker, D.2    Kollman, P.A.3
  • 62
    • 0037139549 scopus 로고    scopus 로고
    • De novo determination of protein backbone structure from residual dipolar couplings using Rosetta
    • Rohl, C. A., and D. Baker. 2002. De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. J. Am. Chem. Soc. 124:2723-2729.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 2723-2729
    • Rohl, C.A.1    Baker, D.2
  • 63
    • 1642464839 scopus 로고    scopus 로고
    • Protein structure prediction using Rosetta
    • Rohl, C. A., C. E. M. Strauss, ., D. Baker. 2004. Protein structure prediction using Rosetta. Methods Enzymol. 383:66-93.
    • (2004) Methods Enzymol. , vol.383 , pp. 66-93
    • Rohl, C.A.1    Strauss, C.E.M.2    Baker, D.3
  • 64
    • 57949105676 scopus 로고    scopus 로고
    • Biclustering via optimal re-ordering of data matrices in systems biology: Rigorous methods and comparative studies
    • DiMaggio, Jr., P. A., S. R. McAllister, ., H. A. Rabitz. 2008. Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies. BMC Bioinformatics. 9:458.
    • (2008) BMC Bioinformatics. , vol.9 , pp. 458
    • DiMaggio Jr., P.A.1    McAllister, S.R.2    Rabitz, H.A.3
  • 65
    • 77954762860 scopus 로고    scopus 로고
    • A network flow model for biclustering via optimal re-ordering of data matrices
    • DiMaggio, P. A., S. R. McAllister, ., H. A. Rabitz. 2010. A network flow model for biclustering via optimal re-ordering of data matrices. J. Glob. Optim. 47:343-354.
    • (2010) J. Glob. Optim. , vol.47 , pp. 343-354
    • Dimaggio, P.A.1    McAllister, S.R.2    Rabitz., H.A.3
  • 66
    • 21644489506 scopus 로고    scopus 로고
    • CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock
    • Daily, M. D., D. Masica,., J. J. Gray. 2005. CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock. Proteins. 60:181-186.
    • (2005) Proteins. , vol.60 , pp. 181-186
    • Daily, M.D.1    Masica., D.2    Gray, J.J.3
  • 67
    • 0038697805 scopus 로고    scopus 로고
    • Protein-protein docking predictions for the CAPRI experiment
    • Gray, J. J., S. E. Moughon,., D. Baker. 2003. Protein-protein docking predictions for the CAPRI experiment. Proteins. 52:118-122.
    • (2003) Proteins. , vol.52 , pp. 118-122
    • Gray, J.J.1    Moughon, S.E.2    Baker, D.3
  • 68
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and sidechain conformations
    • Gray, J. J., S. Moughon, ., D. Baker. 2003. Protein-protein docking with simultaneous optimization of rigid-body displacement and sidechain conformations. J. Mol. Biol. 331:281-299.
    • (2003) J. Mol. Biol. , vol.331 , pp. 281-299
    • Gray, J.J.1    Moughon, S.2    Baker, D.3
  • 69
    • 0034641749 scopus 로고    scopus 로고
    • Native protein sequences are close to optimal for their structures
    • Kuhlman, B., and D. Baker. 2000. Native protein sequences are close to optimal for their structures. Proc. Natl. Acad. Sci. USA. 97:10383-10388.
    • (2000) Proc. Natl. Acad. Sci. USA. , vol.97 , pp. 10383-10388
    • Kuhlman, B.1    Baker, D.2
  • 70
    • 10744230171 scopus 로고    scopus 로고
    • Novel single-cell-level phenotypic assay for residual drug susceptibility and reduced replication capacity of drug-resistant human immunodeficiency virus type 1
    • Zhang, H., Y. Zhou, ., R. F. Siliciano. 2004. Novel single-cell-level phenotypic assay for residual drug susceptibility and reduced replication capacity of drug-resistant human immunodeficiency virus type 1. J. Virol. 78:1718-1729.
    • (2004) J. Virol. , vol.78 , pp. 1718-1729
    • Zhang, H.1    Zhou, Y.2    Siliciano, R.F.3
  • 71
    • 3342981347 scopus 로고    scopus 로고
    • Evolution of genotypic and phenotypic resistance to Enfuvirtide in HIV-infected patients experiencing prolonged virologic failure
    • Poveda, E., B. Rodés,., V. Soriano. 2004. Evolution of genotypic and phenotypic resistance to Enfuvirtide in HIV-infected patients experiencing prolonged virologic failure. J. Med. Virol. 74:21-28.
    • (2004) J. Med. Virol. , vol.74 , pp. 21-28
    • Poveda, E.1    Rodés., B.2    Soriano, V.3
  • 72
    • 33646453478 scopus 로고    scopus 로고
    • Neutralizing antibodies do not mediate suppression of human immunodeficiency virus type 1 in elite suppressors or selection of plasma virus variants in patients on highly active antiretroviral therapy
    • Bailey, J. R., K. G. Lassen,., R. F. Siliciano. 2006. Neutralizing antibodies do not mediate suppression of human immunodeficiency virus type 1 in elite suppressors or selection of plasma virus variants in patients on highly active antiretroviral therapy. J. Virol. 80:4758-4770.
    • (2006) J. Virol. , vol.80 , pp. 4758-4770
    • Bailey, J.R.1    Lassen., K.G.2    Siliciano, R.F.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.