메뉴 건너뛰기




Volumn 2, Issue 3-4, 2008, Pages 105-113

PROTDES: CHARMM toolbox for computational protein design

Author keywords

CHARMM; Computational protein design; Solvation models; Synthetic biology

Indexed keywords


EID: 77649187057     PISSN: 18725325     EISSN: 18725333     Source Type: Journal    
DOI: 10.1007/s11693-009-9026-7     Document Type: Article
Times cited : (9)

References (38)
  • 1
    • 29144468591 scopus 로고    scopus 로고
    • A residue-pairwise generalized born scheme, suitable for protein design simulations
    • Archontis G, Simonson T (2005) A residue-pairwise generalized born scheme, suitable for protein design simulations. J Phys Chem B 109: 22667-22673.
    • (2005) J Phys Chem B , vol.109 , pp. 22667-22673
    • Archontis, G.1    Simonson, T.2
  • 2
    • 0026657433 scopus 로고
    • Refined 1.8 angstrom crystal structure of the lambda repressor operator complex
    • Beamer L, Pabo C (1992) Refined 1. 8 angstrom crystal structure of the lambda repressor operator complex. J Mol Biol 227: 177-196.
    • (1992) J Mol Biol , vol.227 , pp. 177-196
    • Beamer, L.1    Pabo, C.2
  • 3
    • 0035807809 scopus 로고    scopus 로고
    • Enzyme-like proteins by computational design
    • Bolon D, Mayo S (2001) Enzyme-like proteins by computational design. Proc Natl Acad Sci USA 98: 14274-14279.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 14274-14279
    • Bolon, D.1    Mayo, S.2
  • 4
    • 0025830469 scopus 로고
    • A method to identify protein sequences folding into a known three-dimensional structure
    • Bowie J, Lathy R, Heisenberg D (1991) A method to identify protein sequences folding into a known three-dimensional structure. Science 253: 164-170.
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.1    Lathy, R.2    Heisenberg, D.3
  • 6
    • 48249136625 scopus 로고    scopus 로고
    • Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms
    • Cheng TMK, Lu Y-E, Vendruscolo M, Pietro L, Blundell TL (2008) Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms. PLoS Comput Biol 4(7): e1000135.
    • (2008) PLoS Comput Biol , vol.4 , Issue.7
    • Cheng, T.M.K.1    Lu, Y.-E.2    Vendruscolo, M.3    Pietro, L.4    Blundell, T.L.5
  • 8
    • 0029920337 scopus 로고    scopus 로고
    • Protein design automation
    • Dahiyat B, Mayo S (1996) Protein design automation. Protein Sci 5: 895-903.
    • (1996) Protein Science , vol.5 , pp. 895-903
    • Dahiyat, B.1    Mayo, S.2
  • 9
    • 0031558762 scopus 로고    scopus 로고
    • De-novo protein design: Towards fully automated sequence selection
    • Dahiyat C, Sarisky BI, Mayo S (1997) De-novo protein design: towards fully automated sequence selection. J Mol Biol 273(4): 789-796.
    • (1997) J Mol Biol , vol.273 , Issue.4 , pp. 789-796
    • Dahiyat, C.1    Sarisky, B.I.2    Mayo, S.3
  • 11
    • 0033516509 scopus 로고    scopus 로고
    • Hydrophobic core design and structure prediction with backbone flexibility
    • Desjarlais JR, Handel TM (1999) Hydrophobic core design and structure prediction with backbone flexibility. J Mol Biol 189: 305-318.
    • (1999) J Mol Biol , vol.189 , pp. 305-318
    • Desjarlais, J.R.1    Handel, T.M.2
  • 12
    • 0028871798 scopus 로고
    • Side-chain conformational entropy in protein folding
    • Doig AJ, Sternberg MJE (1995) Side-chain conformational entropy in protein folding. Protein Sci 4: 2247-2251.
    • (1995) Protein Sci , vol.4 , pp. 2247-2251
    • Doig, A.J.1    Sternberg, M.J.E.2
  • 13
    • 0028429178 scopus 로고
    • Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains
    • Dunbrack RL, Karplus M (1994) Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains. Nat Struct Biol 1(5): 334-340.
    • (1994) Nat Struct Biol , vol.1 , Issue.5 , pp. 334-340
    • Dunbrack, R.L.1    Karplus, M.2
  • 14
    • 44949215646 scopus 로고    scopus 로고
    • Prediction of binding sites in receptor-ligand complexes with the gaussian network model
    • Haliloglu T, Seyrek E, Erman B (2008) Prediction of binding sites in receptor-ligand complexes with the gaussian network model. Phys Rev Lett 100(22): 228102-228106.
    • (2008) Phys Rev Lett , vol.100 , Issue.22 , pp. 228102-228106
    • Haliloglu, T.1    Seyrek, E.2    Erman, B.3
  • 15
    • 0040914011 scopus 로고
    • P-σ-π analysis. a method for the correlation of biological activity and chemical structurecomputational design of a biologically active enzyme
    • Hansch C, Fujita T (1964) p-σ-π analysis. a method for the correlation of biological activity and chemical structurecomputational design of a biologically active enzyme. J Am Chem Soc 86: 1616-1626.
    • (1964) J Am Chem Soc , vol.86 , pp. 1616-1626
    • Hansch, C.1    Fujita, T.2
  • 16
    • 0028237287 scopus 로고
    • Optimal sequence selection in proteins of known structure by simulated evolution
    • Hellinga HW, Richards FM (1994) Optimal sequence selection in proteins of known structure by simulated evolution. Proc Nat Acad Sci USA 91(13): 5803-5807.
    • (1994) Proc Nat Acad Sci USA , vol.91 , Issue.13 , pp. 5803-5807
    • Hellinga, H.W.1    Richards, F.M.2
  • 17
    • 33846001986 scopus 로고    scopus 로고
    • Conformational sampling with implicit solvent models: Application to the phf6 peptide in tau protein
    • Huang C, Stultz A (2007) Conformational sampling with implicit solvent models: application to the phf6 peptide in tau protein. Biophys J 92: 34-45.
    • (2007) Biophys J , vol.92 , pp. 34-45
    • Huang, C.1    Stultz, A.2
  • 18
    • 11244318120 scopus 로고    scopus 로고
    • Computational protein design is a challenge for implicit solvation models
    • Jaramillo A, Wodak SJ (2005) Computational protein design is a challenge for implicit solvation models. Biophys J 88(1): 156-171.
    • (2005) Biophys J , vol.88 , Issue.1 , pp. 156-171
    • Jaramillo, A.1    Wodak, S.J.2
  • 19
    • 0037108748 scopus 로고    scopus 로고
    • Folding free energy function selects native-like protein sequences in the core but not on the surface
    • Jaramillo A, Wernisch L, Hery S, Wodak S (2002) Folding free energy function selects native-like protein sequences in the core but not on the surface. Proc Nat Acad Sci USA 99(21): 13554-13559.
    • (2002) Proc Nat Acad Sci USA , vol.99 , Issue.21 , pp. 13554-13559
    • Jaramillo, A.1    Wernisch, L.2    Hery, S.3    Wodak, S.4
  • 20
    • 0034641749 scopus 로고    scopus 로고
    • Native protein sequences are close to optimal for their structures
    • Kuhlman B, Baker D (2000) Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci USA 97(19): 10383-10388.
    • (2000) Proc Natl Acad Sci U S A , vol.97 , Issue.19 , pp. 10383-10388
    • Kuhlman, B.1    Baker, D.2
  • 21
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • Lazaridis T, Karplus M (1999) Effective energy function for proteins in solution. Proteins 35(3): 133-152.
    • (1999) Proteins , vol.35 , Issue.3 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 24
    • 0038752617 scopus 로고    scopus 로고
    • Computational design of receptor and sensor proteins with novel functions
    • Looger LL, Dwyer MA, Smith JJ, Hellinga HW (2003) Computational design of receptor and sensor proteins with novel functions. Nature 423(6936): 185-190.
    • (2003) Nature , vol.423 , Issue.6936 , pp. 185-190
    • Looger, L.L.1    Dwyer, M.A.2    Smith, J.J.3    Hellinga, H.W.4
  • 25
    • 34248586877 scopus 로고    scopus 로고
    • Computational sidechain placement and protein mutagenesis with implicit solvent models
    • Lopes A, Alexandrov A, Bathelt C, Archontis G, Simonson T (2007) Computational sidechain placement and protein mutagenesis with implicit solvent models. Proteins 67(4): 853-867.
    • (2007) Proteins , vol.67 , Issue.4 , pp. 853-867
    • Lopes, A.1    Alexandrov, A.2    Bathelt, C.3    Archontis, G.4    Simonson, T.5
  • 26
    • 0345827608 scopus 로고    scopus 로고
    • Sequence determinants of amyloid fibril formation
    • López de la Paz M, Serrano L (2004) Sequence determinants of amyloid fibril formation. Proc Natl Acad Sci USA 101(1): 87-92.
    • (2004) Proc Natl Acad Sci USA , vol.101 , Issue.1 , pp. 87-92
    • López de la Paz, M.1    Serrano, L.2
  • 27
    • 0028943275 scopus 로고
    • The 3-dimensional structure of peptide-mhc complexes
    • Madden DR (1995) The 3-dimensional structure of peptide-mhc complexes. Annu Rev Immunol 13: 587-622.
    • (1995) Annu Rev Immunol , vol.13 , pp. 587-622
    • Madden, D.R.1
  • 28
    • 0027525106 scopus 로고
    • The antigenic identity of peptide-mhc complexes: A comparison of the conformations of five viral peptides presented by hla-
    • Madden DR, Garboczi DN, Wiley D (1993) The antigenic identity of peptide-mhc complexes: a comparison of the conformations of five viral peptides presented by hla-. Cell 75: 693-708.
    • (1993) Cell , vol.75 , pp. 693-708
    • Madden, D.R.1    Garboczi, D.N.2    Wiley, D.3
  • 30
    • 0023338543 scopus 로고
    • Accesible surface areas as a measure of the thermodynamics parameters of hydration of peptides
    • Ooi T, Oobatake M, Nemethy G, Scheraga H (1987) Accesible surface areas as a measure of the thermodynamics parameters of hydration of peptides. Proc Natl Acad Sci USA 84: 3086-3090.
    • (1987) Proc Natl Acad Sci USA , vol.84 , pp. 3086-3090
    • Ooi, T.1    Oobatake, M.2    Nemethy, G.3    Scheraga, H.4
  • 34
    • 33644949935 scopus 로고    scopus 로고
    • Recapitulation and design of protein binding peptide structures and sequences
    • Sood V, Baker D (2006) Recapitulation and design of protein binding peptide structures and sequences. J Mol Biol 357: 917-927.
    • (2006) J Mol Biol , vol.357 , pp. 917-927
    • Sood, V.1    Baker, D.2
  • 35
    • 0030762021 scopus 로고    scopus 로고
    • Coupling backbone flexibility and amino acid sequence selection in protein design
    • Su A, Mayo SL (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
  • 36
    • 47149096704 scopus 로고    scopus 로고
    • CHARMM-GUI: A web-based graphical user interface for CHARMM
    • Sunhwan J, Taehoon K, Vidyashankara GI, Wonpil I (2008) CHARMM-GUI: a web-based graphical user interface for CHARMM. J Comput Chem 29(11): 1859-1865.
    • (2008) J Comput Chem , vol.29 , Issue.11 , pp. 1859-1865
    • Sunhwan, J.1    Taehoon, K.2    Vidyashankara, G.I.3    Wonpil, I.4
  • 38
    • 0034682869 scopus 로고    scopus 로고
    • Automatic protein design with all atom force-fields by exact and heuristic optimization
    • Wernisch L, Hery S, Wodak S (2000) Automatic protein design with all atom force-fields by exact and heuristic optimization. J Mol Biol 301(3): 713-736.
    • (2000) J Mol Biol , vol.301 , Issue.3 , pp. 713-736
    • Wernisch, L.1    Hery, S.2    Wodak, S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.