메뉴 건너뛰기




Volumn 24, Issue 2-3, 2005, Pages 109-130

A deterministic optimization approach to protein sequence design using continuous models

Author keywords

Deterministic optimization; Graph spectral method; Inverse folding; Lattice models; Protein sequence design

Indexed keywords

ALGORITHMS; CHEMICAL BONDS; COMPUTATIONAL COMPLEXITY; CONFORMATIONS; DATABASE SYSTEMS; HYDROPHOBICITY; LATTICE CONSTANTS; OPTIMIZATION; PHYSIOLOGICAL MODELS; PROGRAM PROCESSORS;

EID: 13444306463     PISSN: 02783649     EISSN: None     Source Type: Journal    
DOI: 10.1177/0278364905050354     Document Type: Article
Times cited : (18)

References (43)
  • 1
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen, C. 1973. Principles that govern the folding of protein chains. Science 181(4096):223-230.
    • (1973) Science , vol.181 , Issue.4096 , pp. 223-230
    • Anfinsen, C.1
  • 2
    • 0033497009 scopus 로고    scopus 로고
    • Dynamics of proteins and biomolecular complexes: Inferring functional motions from structure
    • Bahar, I. 1999. Dynamics of proteins and biomolecular complexes: inferring functional motions from structure. Reviews in Chemical Engineering 15(4):319-347.
    • (1999) Reviews in Chemical Engineering , vol.15 , Issue.4 , pp. 319-347
    • Bahar, I.1
  • 3
    • 0037847500 scopus 로고    scopus 로고
    • Geometrical approach to protein folding: A tube picture
    • Banavar, J. R., and Maritan, A. M. 2003. Geometrical approach to protein folding: a tube picture. Reviews of Modern Physics 75:23-34.
    • (2003) Reviews of Modern Physics , vol.75 , pp. 23-34
    • Banavar, J.R.1    Maritan, A.M.2
  • 5
    • 0001241926 scopus 로고    scopus 로고
    • Material interpolations in topology optimization
    • Bendsøe, M. P., and Sigmund, O. 1999. Material interpolations in topology optimization. Archive of Applied Mechanics 69:645-654.
    • (1999) Archive of Applied Mechanics , vol.69 , pp. 645-654
    • Bendsøe, M.P.1    Sigmund, O.2
  • 8
    • 0032725441 scopus 로고    scopus 로고
    • Folding alphabets
    • Chan, H. S. 1999. Folding alphabets. Nature Structural Biology 6(11):994-996.
    • (1999) Nature Structural Biology , vol.6 , Issue.11 , pp. 994-996
    • Chan, H.S.1
  • 9
    • 0027122748 scopus 로고
    • One thousand families for the molecular biologist
    • Chothia, C. 1992. One thousand families for the molecular biologist. Nature 357:543-544.
    • (1992) Nature , vol.357 , pp. 543-544
    • Chothia, C.1
  • 10
    • 0028858499 scopus 로고
    • De novo design of the hydrophobic cores of proteins
    • Desjarlais, J. R., and Handel, T. M. 1995. De novo design of the hydrophobic cores of proteins. Protein Science 4:2006-2018.
    • (1995) Protein Science , vol.4 , pp. 2006-2018
    • Desjarlais, J.R.1    Handel, T.M.2
  • 11
    • 0026589733 scopus 로고
    • The dead-end elimination theorem and its use in protein side-chain positioning
    • Desmet, J., De Maeyer, M., Hazes, B., and Lasters, I. 1992. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 356:539-542.
    • (1992) Nature , vol.356 , pp. 539-542
    • Desmet, J.1    De Maeyer, M.2    Hazes, B.3    Lasters, I.4
  • 12
    • 4243719017 scopus 로고    scopus 로고
    • New algorithm for protein design
    • Deutsche, J. M., and Kurosky, T. 1996. New algorithm for protein design. Physical Review Letters 76(2):323-326.
    • (1996) Physical Review Letters , vol.76 , Issue.2 , pp. 323-326
    • Deutsche, J.M.1    Kurosky, T.2
  • 16
    • 0028237287 scopus 로고
    • Optimal selection of sequences f proteins of known structure by simulated evolution
    • Hellinga, H. W., and Richards, F. M. 1994. Optimal selection of sequences f proteins of known structure by simulated evolution. Proceedings of the National Academy of Sciences 91:5803-5807.
    • (1994) Proceedings of the National Academy of Sciences , vol.91 , pp. 5803-5807
    • Hellinga, H.W.1    Richards, F.M.2
  • 18
    • 13944274522 scopus 로고    scopus 로고
    • Design of HP models of proteins by energy gap criterion using continuous modeling and optimization
    • Salt Lake City, UT, September
    • Koh, S. K., and Ananthasuresh, G. K. 2004. Design of HP models of proteins by energy gap criterion using continuous modeling and optimization. Proceedings of the ASME IDETC 2004 Mechanisms and Robotics Conference, Salt Lake City, UT, September.
    • (2004) Proceedings of the ASME IDETC 2004 Mechanisms and Robotics Conference
    • Koh, S.K.1    Ananthasuresh, G.K.2
  • 19
    • 0024750637 scopus 로고
    • A lattice statistical mechanics model of the conformational and sequence spaces of proteins
    • Lau, K. F., and Dill, K. A. 1989. A lattice statistical mechanics model of the conformational and sequence spaces of proteins. Macromolecules 22:3986.
    • (1989) Macromolecules , vol.22 , pp. 3986
    • Lau, K.F.1    Dill, K.A.2
  • 20
    • 0029772552 scopus 로고    scopus 로고
    • Emergence of preferred structures in a simple model of protein folding
    • Li, H., Helling, R., Tang, C., and Wingreen, N. S. 1996. Emergence of preferred structures in a simple model of protein folding. Science 273:666-669.
    • (1996) Science , vol.273 , pp. 666-669
    • Li, H.1    Helling, R.2    Tang, C.3    Wingreen, N.S.4
  • 21
    • 7044220745 scopus 로고    scopus 로고
    • Nature of driving force for protein folding: A result from analyzing the statistical potential
    • Li, H., Tang, C., and Wingreen, N. S. 1997. Nature of driving force for protein folding: a result from analyzing the statistical potential. Physical Review Letters 79(4):765-768.
    • (1997) Physical Review Letters , vol.79 , Issue.4 , pp. 765-768
    • Li, H.1    Tang, C.2    Wingreen, N.S.3
  • 22
    • 0037110580 scopus 로고    scopus 로고
    • Designability of protein structures: A lattice-model study using the Miyazawa-Jernigan matrix
    • Li, H., Tang, C., and Wingreen, N. S. 2002. Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix. Proteins: Structure, Function, and Genetics. 49:403-412.
    • (2002) Proteins: Structure, Function, and Genetics , vol.49 , pp. 403-412
    • Li, H.1    Tang, C.2    Wingreen, N.S.3
  • 23
    • 33845377127 scopus 로고
    • Estimation of effective inter-residue contact energies from protein crystal structures: Quasi-chemical approximation
    • Miyazawa, S., and Jernigan, R. L. 1985. Estimation of effective inter-residue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 18: 534-552.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 24
    • 0021108287 scopus 로고
    • Designing proteins and peptides
    • Pabo, C. 1983. Designing proteins and peptides. Nature 301(5897):200.
    • (1983) Nature , vol.301 , Issue.5897 , pp. 200
    • Pabo, C.1
  • 26
    • 0033955344 scopus 로고    scopus 로고
    • Backbone cluster identification in proteins by a graph theoretical method
    • Patra, S. M., and Vishveshwara, S. 2000. Backbone cluster identification in proteins by a graph theoretical method. Biophysical Chemistry 84:13-26.
    • (2000) Biophysical Chemistry , vol.84 , pp. 13-26
    • Patra, S.M.1    Vishveshwara, S.2
  • 27
    • 21844461156 scopus 로고    scopus 로고
    • Convex global underestimation
    • Migdalas, A., editor. Kluwer Academic, Dordrecht
    • Phillips, A. T., Rosen, J. B, and Dill, K. A. 2001. Convex global underestimation. From Local to Global Optimization, Migdalas, A., editor. Kluwer Academic, Dordrecht, pp. 1-18.
    • (2001) From Local to Global Optimization , pp. 1-18
    • Phillips, A.T.1    Rosen, J.B.2    Dill, K.A.3
  • 28
    • 0023155210 scopus 로고
    • Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes
    • Ponder, J. W., and Richards, F. M. 1987. Tertiary templates for proteins: use of packing criteria in the enumeration of allowed sequences for different structural classes. Journal of Molecular Biology 193:775-791.
    • (1987) Journal of Molecular Biology , vol.193 , pp. 775-791
    • Ponder, J.W.1    Richards, F.M.2
  • 30
    • 0028270634 scopus 로고
    • Kinetics of protein folding: A lattice model study of the requirements for folding to the native state
    • Sali, A., Shakhnovich, E., and Karplus, M. 1994. Kinetics of protein folding: a lattice model study of the requirements for folding to the native state. Journal of Molecular Biology 235:1614-1636.
    • (1994) Journal of Molecular Biology , vol.235 , pp. 1614-1636
    • Sali, A.1    Shakhnovich, E.2    Karplus, M.3
  • 31
    • 0035105547 scopus 로고    scopus 로고
    • Sequence design in lattice models by graph theoretical methods
    • Sanjeev, B. S., Patra, S. M., and Vishveshwara, S. 2001. Sequence design in lattice models by graph theoretical methods. Journal of Chemical Physics 114(4):1904-1914.
    • (2001) Journal of Chemical Physics , vol.114 , Issue.4 , pp. 1904-1914
    • Sanjeev, B.S.1    Patra, S.M.2    Vishveshwara, S.3
  • 33
    • 0031561289 scopus 로고    scopus 로고
    • Statistical mechanics of the combinatorial synthesis and analysis of folding macromolecules
    • Saven, J. G., and Wolynes, P. G. 1997. Statistical mechanics of the combinatorial synthesis and analysis of folding macromolecules. Journal of Physics and Chemistry B 101:8375-8389.
    • (1997) Journal of Physics and Chemistry B , vol.101 , pp. 8375-8389
    • Saven, J.G.1    Wolynes, P.G.2
  • 35
    • 0036891794 scopus 로고    scopus 로고
    • A multiphase level set framework for image segmentation using the Mumford and Shah model
    • Vese, L. A., and Chan, T. F. 2002. A multiphase level set framework for image segmentation using the Mumford and Shah model. International Journal of Computer Vision 50(3):271-293.
    • (2002) International Journal of Computer Vision , vol.50 , Issue.3 , pp. 271-293
    • Vese, L.A.1    Chan, T.F.2
  • 37
    • 0032726679 scopus 로고    scopus 로고
    • A computational approach to simplifying the protein folding alphabet
    • Wang, J., and Wang, W. 1999. A computational approach to simplifying the protein folding alphabet. Nature Structural Biology 6(11):1033-1038.
    • (1999) Nature Structural Biology , vol.6 , Issue.11 , pp. 1033-1038
    • Wang, J.1    Wang, W.2
  • 39
    • 0035727235 scopus 로고    scopus 로고
    • Topology optimization of compliant mechanisms with multiple materials using a peak function material interpolation scheme
    • Yin, L., and Ananthasuresh, G. K. 2001. Topology optimization of compliant mechanisms with multiple materials using a peak function material interpolation scheme. Structural and Multidisciplinary Optimization 23(1):49-62.
    • (2001) Structural and Multidisciplinary Optimization , vol.23 , Issue.1 , pp. 49-62
    • Yin, L.1    Ananthasuresh, G.K.2
  • 40
    • 0036544395 scopus 로고    scopus 로고
    • Novel design technique for electrothermally actuated compliant micromechanisms
    • Yin, L., and Ananthasuresh, G. K. 2002. Novel design technique for electrothermally actuated compliant micromechanisms. Sensors and Actuators A 97/98:599-609.
    • (2002) Sensors and Actuators A , vol.97-98 , pp. 599-609
    • Yin, L.1    Ananthasuresh, G.K.2
  • 41
    • 0035416177 scopus 로고    scopus 로고
    • Optimality criteria method for the topology optimization under multiple constraints
    • Yin, L., and Yang, W. 2001. Optimality criteria method for the topology optimization under multiple constraints. Computers and Structures 79:1839-1850.
    • (2001) Computers and Structures , vol.79 , pp. 1839-1850
    • Yin, L.1    Yang, W.2
  • 43
    • 0034635349 scopus 로고    scopus 로고
    • Statistical theory of combinatorial libraries of folding proteins: Energetic discrimination of a target structure
    • Zou, J., and Saven, J. G. 2000. Statistical theory of combinatorial libraries of folding proteins: energetic discrimination of a target structure. Journal of Molecular Biology 296:281-294.
    • (2000) Journal of Molecular Biology , vol.296 , pp. 281-294
    • Zou, J.1    Saven, J.G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.