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Volumn 234, Issue 3, 1993, Pages 779-815

Comparative protein modelling by satisfaction of spatial restraints

Author keywords

Comparative protein modelling; Optimization; Protein database; Restraints; Serine proteinases

Indexed keywords


EID: 0027136282     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1993.1626     Document Type: Article
Times cited : (10889)

References (110)
  • 2
    • 0026723852 scopus 로고
    • Use of a potential of mean force to analyze free energy contributions in protein folding
    • Avbelj, F. (1992). Use of a potential of mean force to analyze free energy contributions in protein folding. Biochemistry, 31, 6290-6297.
    • (1992) Biochemistry , vol.31 , pp. 6290-6297
    • Avbelj, F.1
  • 3
    • 0026439783 scopus 로고
    • Application of a directed conformational search for generating.‘i-D coordinates for protein structures from a-carbon coordinates
    • Bassolino-Klimas, D. & Bruccoleri, R. E. (1992). Application of a directed conformational search for generating.‘i-D coordinates for protein structures from a-carbon coordinates. Proteins, 14, 465-474.
    • (1992) Proteins , vol.14 , pp. 465-474
    • Bassolino-Klimas, D.1    Bruccoleri, R.E.2
  • 4
    • 0024373677 scopus 로고
    • Two-dimensional NMR and protein structure
    • Bax, A. (1989). Two-dimensional NMR and protein structure. Annu. Rev. Biochem. 58, 223-256.
    • (1989) Annu. Rev. Biochem. , vol.58 , pp. 223-256
    • Bax, A.1
  • 8
    • 0022341314 scopus 로고
    • Computer-aided design in protein engineering
    • Blundell, T. L. & Sternberg, M. J. E. (1985). Computer-aided design in protein engineering. Trends Biotechnol. 3, 228-235.
    • (1985) Trends Biotechnol , vol.3 , pp. 228-235
    • Blundell, T.L.1    Sternberg, M.J.E.2
  • 10
    • 0023305986 scopus 로고
    • Knowledge-based prediction of protein structures and the design of novel molecules
    • Blundell, T. L., Sibanda, B. L., Sternberg, M. J. E. & Thornton, J. M. (1987). Knowledge-based prediction of protein structures and the design of novel molecules. Nature (London), 326, 347-352.
    • (1987) Nature (London) , vol.326 , pp. 347-352
    • Blundell, T.L.1    Sibanda, B.L.2    Sternberg, M.J.E.3    Thornton, J.M.4
  • 11
    • 0025155981 scopus 로고
    • A novel approach to prediction of the 3-dimensional structures of protein backbones by neural networks
    • Bohr, H., Bohr, J. Brunak, S., Cotterill, R. M. J., Fredholm, H., Lautrup, B. & Petersen, S. B. (1990). A novel approach to prediction of the 3-dimensional structures of protein backbones by neural networks. FEBS Letters, 261, 43-46.
    • (1990) FEBS Letters , vol.261 , pp. 43-46
    • Bohr, H.1    Bohr Brunak, J.S.2    Cotterill, R.M.J.3    Fredholm, H.4    Lautrup, B.5    Petersen, S.B.6
  • 12
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie, J. U., Liitthy, R. & Eisenberg, D. (1991). A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253, 164-170.
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Liitthy, R.2    Eisenberg, D.3
  • 13
    • 0022336792 scopus 로고
    • Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm
    • Braun, W. & Go, N. (1985). Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm. J. Mol. Biol. 186, 611-626.
    • (1985) J. Mol. Biol. , vol.186 , pp. 611-626
    • Braun, W.1    Go, N.2
  • 16
    • 0014693695 scopus 로고
    • A possible three-dimensional structure of bovine a-lactalbumin based on that of hen’s egg-white lysozyme
    • Browne, W. J., North, A. C. T., Phillips, D. C., Brew, K., Vanaman, T. C. & Hill, R. C. (1969). A possible three-dimensional structure of bovine a-lactalbumin based on that of hen’s egg-white lysozyme. J. Mol. Biol. 42, 65-86.
    • (1969) J. Mol. Biol. , vol.42 , pp. 65-86
    • Browne, W.J.1    North, A.C.T.2    Phillips, D.C.3    Brew, K.4    Vanaman, T.C.5    Hill, R.C.6
  • 17
    • 0023173201 scopus 로고
    • Prediction of the folding of short polypeptide segments by uniform conformational sampling
    • Bruccoleri, R. E. & Karplus, M. (1987). Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers, 26, 137-168.
    • (1987) Biopolymers , vol.26 , pp. 137-168
    • Bruccoleri, R.E.1    Karplus, M.2
  • 18
    • 0023090541 scopus 로고
    • Solution of a protein crystal structure with a model obtained from NMR interproton distance restraints
    • Briinger, A. T., Campbell, R. L., Clore, G. M., Gronenborn, A. M., Karplus, M., Petsko, G. A. & Teeter, M. M. (1987a). Solution of a protein crystal structure with a model obtained from NMR interproton distance restraints. Science, 235, 1049-1053.
    • (1987) Science , vol.235 , pp. 1049-1053
    • Briinger, A.T.1    Campbell, R.L.2    Clore, G.M.3    Gronenborn, A.M.4    Karplus, M.5    Petsko, G.A.6    Teeter, M.M.7
  • 19
    • 0023140814 scopus 로고
    • Crystallographic R-factor refinement by molecular dynamics
    • Briinger, A. T., Kuriyan, J. & Karplus, M. (1987). Crystallographic R-factor refinement by molecular dynamics. Science, 235, 458-460.
    • (1987) Science , vol.235 , pp. 458-460
    • Briinger, A.T.1    Kuriyan, J.2    Karplus, M.3
  • 20
    • 0026539511 scopus 로고
    • Structure-derived hydro-phobic potential: Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds
    • Casari, G. & Sippl, M. J. (1992). Structure-derived hydro-phobic potential: hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds, J. Mol. Biol. 224, 725-732.
    • (1992) J. Mol. Biol. , vol.224 , pp. 725-732
    • Casari, G.1    Sippl, M.J.2
  • 21
    • 0027122748 scopus 로고
    • One thousand families for the molecular biologist
    • Chothia, C. (1992). One thousand families for the molecular biologist. Nature (London), 360, 543-544.
    • (1992) Nature (London) , vol.360 , pp. 543-544
    • Chothia, C.1
  • 23
    • 0015987426 scopus 로고
    • Prediction of protein conformation
    • Chou, P. Y. & Fasman, G. D. (1974). Prediction of protein conformation. Biochemistry, 13, 222-245.
    • (1974) Biochemistry , vol.13 , pp. 222-245
    • Chou, P.Y.1    Fasman, G.D.2
  • 24
    • 0024527223 scopus 로고
    • Modelling the polypeptide backbone with “spare parts” from known protein structures
    • Claessens, M., Cutsem, E. V., Easters, I. & Wodak, S. (1989). Modelling the polypeptide backbone with “spare parts” from known protein structures. Protein Eng. 4, 335-345.
    • (1989) Protein Eng , vol.4 , pp. 335-345
    • Claessens, M.1    Cutsem, E.V.2    Easters, I.3    Wodak, S.4
  • 25
    • 0025757134 scopus 로고
    • Two-, three-, and four-dimensional NMR methods for obtaining larger and more precise three-dimensional structures of proteins in solution
    • Clore, G. M. & Gronenborn, A. M. (1991). Two-, three-, and four-dimensional NMR methods for obtaining larger and more precise three-dimensional structures of proteins in solution. Annu. Rev. Biophys. Chem. 20, 29-63.
    • (1991) Annu. Rev. Biophys. Chem , vol.20 , pp. 29-63
    • Clore, G.M.1    Gronenborn, A.M.2
  • 26
    • 0023008905 scopus 로고
    • Application of molecular dynamics with interproton distance restraints to 3D protein structure determination
    • Clore, G. M., Briinger, A. T., Karplus, M. & Gronenborn, A. M. (1986). Application of molecular dynamics with interproton distance restraints to 3D protein structure determination. J. Mol. Biol. 191, 523-551.
    • (1986) J. Mol. Biol. , vol.191 , pp. 523-551
    • Clore, G.M.1    Briinger, A.T.2    Karplus, M.3    Gronenborn, A.M.4
  • 28
    • 0025288651 scopus 로고
    • The building of protein structures from a-carbon coordinates
    • Correa, P. E. (1990). The building of protein structures from a-carbon coordinates. Proteins, 7, 366-377.
    • (1990) Proteins , vol.7 , pp. 366-377
    • Correa, P.E.1
  • 29
    • 0000228203 scopus 로고
    • (Dayhoff, M. O., ed.), National Biomedical Research Foundation, Washington, DC
    • Dayhoff, M. O., Schwartz, R. M. & Orcutt, B. C. (1978). In Atlas of Protein Sequence and Structure (Dayhoff, M. O., ed.), vol. 5, suppl. 3, pp. 345-352, National Biomedical Research Foundation, Washington, DC.
    • (1978) In Atlas of Protein Sequence and Structure , vol.5 , pp. 345-352
    • Dayhoff, M.O.1    Schwartz, R.M.2    Orcutt, B.C.3
  • 30
    • 0026589733 scopus 로고
    • The dead-end elimination theorem and its use in protein side-chain positioning
    • Desmet, J., De Maeyer, M., Hazes, B. & Easters, I. (1992). The dead-end elimination theorem and its use in protein side-chain positioning. Nature (London), 356, 539-542.
    • (1992) Nature (London) , vol.356 , pp. 539-542
    • Desmet, J.1    De Maeyer, M.2    Hazes, B.3    Easters, I.4
  • 31
    • 84986500316 scopus 로고
    • Protein structure prediction using a combination of sequence homology and global energy minimization, 1, Global energy minimization of surface loops
    • Dudek, M. J. & Scheraga, H. A. (1990). Protein structure prediction using a combination of sequence homology and global energy minimization, 1, Global energy minimization of surface loops. J. Comp. Chem. 11, 121-151.
    • (1990) J. Comp. Chem. , vol.11 , pp. 121-151
    • Dudek, M.J.1    Scheraga, H.A.2
  • 32
    • 0027160197 scopus 로고
    • Prediction of protein side-chain conformations from a backbone conformation dependent rotamer library
    • Dunbrack, R. E. & Karplus, M, (1993). Prediction of protein side-chain conformations from a backbone conformation dependent rotamer library. J. Mol. Biol. 230, 543-571.
    • (1993) J. Mol. Biol. , vol.230 , pp. 543-571
    • Dunbrack, R.E.1    Karplus, M.2
  • 34
    • 0026328388 scopus 로고
    • Generalized protein tertiary structure recognition using associative memory Hamiltonians
    • Friedrichs, M. S., Goldstein, R. A. & Wolynes, P. G. (1991). Generalized protein tertiary structure recognition using associative memory Hamiltonians. J. Mol. Biol. 222, 1013-1034.
    • (1991) J. Mol. Biol. , vol.222 , pp. 1013-1034
    • Friedrichs, M.S.1    Goldstein, R.A.2    Wolynes, P.G.3
  • 35
    • 0023192209 scopus 로고
    • Rat submaxillary gland serine protease, tonin. Structure solution and refinement at P8 A resolution
    • Fujinaga, M. & James, M. N G. (1987). Rat submaxillary gland serine protease, tonin. Structure solution and refinement at P8 A resolution. J. Mol. Biol. 195, 373-396.
    • (1987) J. Mol. Biol. , vol.195 , pp. 373-396
    • Fujinaga, M.1    James, M.N.G.2
  • 37
    • 0026726481 scopus 로고
    • Topology fingerprint approach to the inverse protein folding problem
    • Godxik, A., Kolinski, A. & Skolnick, J. (1992). Topology fingerprint approach to the inverse protein folding problem, J. Mol. Biol. 227, 227-238.
    • (1992) J. Mol. Biol. , vol.227 , pp. 227-238
    • Godxik, A.1    Kolinski, A.2    Skolnick, J.3
  • 38
    • 0019888748 scopus 로고
    • Comparative model-building of the mammalian serine proteases
    • Greer, I. (1981). Comparative model-building of the mammalian serine proteases. J. Mol. Biol. 153, 1027-1042.
    • (1981) J. Mol. Biol. , vol.153 , pp. 1027-1042
    • Greer, I.1
  • 39
    • 0025287330 scopus 로고
    • Comparative modelling methods: Application to the family of the mammalian serine proteases
    • Greer, J. (1990). Comparative modelling methods: application to the family of the mammalian serine proteases. Proteins, 7, 317-334.
    • (1990) Proteins , vol.7 , pp. 317-334
    • Greer, J.1
  • 40
    • 0026018780 scopus 로고
    • A new method for building protein conformations from sequence alignments with homologues of known structure
    • Havel, T. F. & Snow, M. E. (1991). A new method for building protein conformations from sequence alignments with homologues of known structure. J. Mol. Biol. 217, 1-7.
    • (1991) J. Mol. Biol. , vol.217 , pp. 1-7
    • Havel, T.F.1    Snow, M.E.2
  • 41
    • 0022429234 scopus 로고
    • An evaluation of the combined use of NMR and distance geometry for the determination of protein conformations in solution
    • Havel, T. & Wuthrich, K. (1985). An evaluation of the combined use of NMR and distance geometry for the determination of protein conformations in solution. J. Mol. Biol. 182, 281-294.
    • (1985) J. Mol. Biol. , vol.182 , pp. 281-294
    • Havel, T.1    Wuthrich, K.2
  • 43
    • 0025978283 scopus 로고
    • Database algorithm for generating protein backbone and side-chain coordinates from Ca trace: Application to model building and detection of co-ordinate errors
    • a trace: application to model building and detection of co-ordinate errors. J. Mol. Biol. 218, 183-194.
    • (1991) J. Mol. Biol. , vol.218 , pp. 183-194
    • Holm, L.1    Sander, C.2
  • 44
    • 0026675799 scopus 로고
    • Fast and simple Monte Carlo algorithm for side chain optimization in proteins: Application to model building by homology
    • Holm, L. & Sander, C. (1992). Fast and simple Monte Carlo algorithm for side chain optimization in proteins: application to model building by homology. Proteins, 14, 213-223.
    • (1992) Proteins , vol.14 , pp. 213-223
    • Holm, L.1    Sander, C.2
  • 45
    • 0027057526 scopus 로고
    • A database of protein structure families with common folding motifs
    • Holm, L., Ouzounis, C., Sander, C., Tuparev, G. & Vriend, G. (1992). A database of protein structure families with common folding motifs. Protein Sci. 1, 1691-1968.
    • (1992) Protein Sci , vol.1 , pp. 1691-1968
    • Holm, L.1    Ouzounis, C.2    Sander, C.3    Tuparev, G.4    Vriend, G.5
  • 46
    • 0000338489 scopus 로고
    • Comparison of solvent inaccessible cores of homologous proteins: Definitions useful for protein modelling
    • Hubbard, T. J. P. & Blundell, T. L. (1987). Comparison of solvent inaccessible cores of homologous proteins: definitions useful for protein modelling. Protein Eng. Vol I, 159-171.
    • (1987) Protein Eng , vol.1 , pp. 159-171
    • Hubbard, T.J.P.1    Blundell, T.L.2
  • 47
    • 0018115846 scopus 로고
    • Conformation of amino acid side-chains in proteins
    • Jania, J., Wodak, S., Levitt, M. & Maigret, B. (1978). Conformation of amino acid side-chains in proteins. J. Mol. Biol. 125, 357-386.
    • (1978) J. Mol. Biol. , vol.125 , pp. 357-386
    • Jania, J.1    Wodak, S.2    Levitt, M.3    Maigret, B.4
  • 48
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones, D. T., Taylor, W. R. & Thornton, J. M. (1992). A new approach to protein fold recognition. Nature (London), 358, 86-89.
    • (1992) Nature (London) , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 49
    • 0000356656 scopus 로고
    • A graphics model building and refinement system for macromolecules
    • Jones, T. A. (1978). A graphics model building and refinement system for macromolecules. J. Appl. Crystallogr. 11, 268-272.
    • (1978) J. Appl. Crystallogr. , vol.11 , pp. 268-272
    • Jones, T.A.1
  • 50
    • 0022701772 scopus 로고
    • Using known substructures in protein model building and crystallography
    • Jones, T. H. & Thirup, S. (1986). Using known substructures in protein model building and crystallography. EMBO J. 5, 819-822.
    • (1986) EMBO J , vol.5 , pp. 819-822
    • Jones, T.H.1    Thirup, S.2
  • 51
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 52
    • 0014966180 scopus 로고
    • IUPAC-IUB commission on biochemical nomenclature. Abbreviations and symbols for the description of the conformation of polypeptide chains
    • Kendrew, J. C., Klyne, W., Lifson, S., Miyazawa, T., Nemethy, G., Phillips, D. C., Ramachandran, G. X. & Scheraga, H, (1970). IUPAC-IUB commission on biochemical nomenclature. Abbreviations and symbols for the description of the conformation of polypeptide chains. J. Mol. Biol. 52, 1-17.
    • (1970) J. Mol. Biol. , vol.52 , pp. 1-17
    • Kendrew, J.C.1    Klyne, W.2    Lifson, S.3    Miyazawa, T.4    Nemethy, G.5    Phillips, D.C.6    Ramachandran, G.X.7    Scheraga, H.8
  • 53
    • 0026019108 scopus 로고
    • Prediction of protein side--hain conformation by packing optimization
    • Lee, C. & Subbiah, S. (1991). Prediction of protein side--hain conformation by packing optimization. J. Mol. Biol. 217, 373-388.
    • (1991) J. Mol. Biol. , vol.217 , pp. 373-388
    • Lee, C.1    Subbiah, S.2
  • 54
    • 0000187138 scopus 로고
    • The response of protein structures to amino-acid sequence changes
    • Lesk, A. M. & Chothia, C. H. (1986). The response of protein structures to amino-acid sequence changes. Phil. Trans. Roy. Soc. Lond. 317, 345-356.
    • (1986) Phil. Trans. Roy. Soc. Lond. , vol.317 , pp. 345-356
    • Lesk, A.M.1    Chothia, C.H.2
  • 55
    • 0021104755 scopus 로고
    • Molecular dynamics of native protein. II. Analysis and nature of motion
    • LevGt, M. (1983). Molecular dynamics of native protein. II. Analysis and nature of motion. J. Mol. Biol. 168, 621-657.
    • (1983) J. Mol. Biol. , vol.168 , pp. 621-657
    • Levgt, M.1
  • 56
    • 0026754015 scopus 로고
    • Accurate modeling of protein conformation by automatic segment matching
    • Levitt, M. (1992). Accurate modeling of protein conformation by automatic segment matching. J. Mol. Biol. 226, 507-533.
    • (1992) J. Mol. Biol. , vol.226 , pp. 507-533
    • Levitt, M.1
  • 58
    • 0026610767 scopus 로고
    • Assessment of protein models wdh three-dimensional profiles
    • Luthy, R., Bowie, J. U. & Eisenberg, D. (1992). Assessment of protein models wdh three-dimensional profiles. Nature (London), 356, 84-85.
    • (1992) Nature (London) , vol.356 , pp. 84-85
    • Luthy, R.1    Bowie, J.U.2    Eisenberg, D.3
  • 59
    • 0025997601 scopus 로고
    • Secondary structure-based profiles: Use of structure-conserving scoring tables in searching protein sequence databases for structural similarities
    • Luthy, R., McLachlan, A. D, & Eisenberg, D. (1991). Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities. Proteins, 10, 229-239.
    • (1991) Proteins , vol.10 , pp. 229-239
    • Luthy, R.1    McLachlan, A.D.2    Eisenberg, D.3
  • 60
    • 0018077908 scopus 로고
    • Hydrophobic character of amino acid residues in globular proteins
    • Manavalan, P. & Ponnuswamy, P. K. (1978). Hydrophobic character of amino acid residues in globular proteins. Nature (London), 275, 673-674.
    • (1978) Nature (London) , vol.275 , pp. 673-674
    • Manavalan, P.1    Ponnuswamy, P.K.2
  • 62
    • 0026492031 scopus 로고
    • Modeling the anti-CEA antibody combining site by homology and conformational search
    • Mas, M. T., Smith, K. C., Yarmush, D. L., Aisaka, K. & Fine, R. M. (1992). Modeling the anti-CEA antibody combining site by homology and conformational search. Proteins, 14, 483-498.
    • (1992) Proteins , vol.14 , pp. 483-498
    • Mas, M.T.1    Smith, K.C.2    Yarmush, D.L.3    Aisaka, K.4    Fine, R.M.5
  • 63
    • 0023521842 scopus 로고
    • Analysis of the relationship between side-chain conformation and secondary structure in globular proteins
    • McGregor, M. J., Islam, S. A. & Sternberg, M. J. E, (1987). Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J. Mol. Biol. 198, 295-310.
    • (1987) J. Mol. Biol. , vol.198 , pp. 295-310
    • McGregor, M.J.1    Islam, S.A.2    Sternberg, M.3
  • 64
    • 0018350099 scopus 로고
    • Gene duplications in the structural evolution of chymotrvpsin
    • McLachlan, A. D. (1979). Gene duplications in the structural evolution of chymotrvpsin. J. Mol. Biol. 128. 49-79.
    • (1979) J. Mol. Biol. , vol.128 , pp. 49-79
    • McLachlan, A.D.1
  • 65
    • 0002104779 scopus 로고
    • Structure of native porcine pancreatic elastase at 165 A resolution
    • Meyer, E., Cole, G., Radakrishnan, R. & Epp, O. (1988). Structure of native porcine pancreatic elastase at 165 A resolution. Ada Crystallogr. sect. B, 44, 26-38.
    • (1988) Ada Crystallogr. Sect. B , vol.44 , pp. 26-38
    • Meyer, E.1    Cole, G.2    Radakrishnan, R.3    Epp, O.4
  • 66
    • 0022788691 scopus 로고
    • An algorithm for determining the conformation of polypeptide segments in proteins by systematic search
    • Moult, J. & James, M. N. G. (1986). An algorithm for determining the conformation of polypeptide segments in proteins by systematic search. Proteins, 1, 146-163.
    • (1986) Proteins , vol.1 , pp. 146-163
    • Moult, J.1    James, M.N.G.2
  • 67
    • 0025104478 scopus 로고
    • Tertiary structural constraints on protein evolutionary diversity; templates, key residues and structure prediction
    • Overington, J., Johnson, M. S., Sali, A. & Blundell, T. L. (1990). Tertiary structural constraints on protein evolutionary diversity; templates, key residues and structure prediction. Proc. Roy. Soc. Lond. sect. B, 241, 132-145.
    • (1990) Proc. Roy. Soc. Lond. Sect. B , vol.241 , pp. 132-145
    • Overington, J.1    Johnson, M.S.2    Sali, A.3    Blundell, T.L.4
  • 68
    • 0027062943 scopus 로고
    • Environment-specific amino acid substitution tables: Tertiary templates and prediction of protein folds
    • Overington, J., Donnelly, O., Johnson, M. S., Sali, A. & Blundell, T, L. (1992). Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds. Protein Sci. 1, 216-226.
    • (1992) Protein Sci , vol.1 , pp. 216-226
    • Overington, J.1    Donnelly, O.2    Johnson, M.S.3    Sali, A.4    Blundell, T.5
  • 70
    • 0026511848 scopus 로고
    • A data bank merging related protein structures and sequences
    • Pascarella, S. & Argos, P. (1992). A data bank merging related protein structures and sequences. Protein Eng. 5, 121-137.
    • (1992) Protein Eng , vol.5 , pp. 121-137
    • Pascarella, S.1    Argos, P.2
  • 71
    • 0027529023 scopus 로고
    • Reconstruction of protein conformations from estimated positions of the Ca coordinates
    • a coordinates. Protein Sci. 2, 315-324.
    • (1993) Protein Sci , vol.2 , pp. 315-324
    • Payne, P.W.1
  • 72
    • 0023155210 scopus 로고
    • Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes
    • Ponder, J. W. & Richards, F. M. (1987). Tertiary templates for proteins: use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol. 193, 775-791.
    • (1987) J. Mol. Biol. , vol.193 , pp. 775-791
    • Ponder, J.W.1    Richards, F.M.2
  • 74
    • 0024570937 scopus 로고
    • Rebuilding flavo-doxin from C. Coordinates: A test study
    • Reid, L. S. & Thornton, J. M. (1989). Rebuilding flavo-doxin from C. coordinates: a test study. Proteins, 5. 170-182.
    • (1989) Proteins , vol.5 , pp. 170-182
    • Reid, L.S.1    Thornton, J.M.2
  • 75
    • 84986513586 scopus 로고
    • Efficient algorithm for the reconstruction of a protein backbone from the a-carbon coordinates
    • Rey, A. & Skolnick, J. (1992). Efficient algorithm for the reconstruction of a protein backbone from the a-carbon coordinates. J. Comp. Chem. 13. 443-456.
    • (1992) J. Comp. Chem. , vol.13 , pp. 443-456
    • Rey, A.1    Skolnick, J.2
  • 76
    • 0017876485 scopus 로고
    • Packing of a-helices. Geometrical constraints and contact areas
    • Richmond, T. J. & Richards, F. M. (1978). Packing of a-helices. Geometrical constraints and contact areas. J. Mol. Biol. 119, 537-555.
    • (1978) J. Mol. Biol. , vol.119 , pp. 537-555
    • Richmond, T.J.1    Richards, F.M.2
  • 77
    • 0006399210 scopus 로고
    • Expert system for protein engineering: Its application in the study of chloramphenicol acetyl transferase and avian pancreatic polypeptide
    • Robson, B., Platt, E., Fishleigh, R. V., Marsden, A. & Millard, P. (1987). Expert system for protein engineering: its application in the study of chloramphenicol acetyl transferase and avian pancreatic polypeptide. J. Mol. Graph. 5, 5-17.
    • (1987) J. Mol. Graph. , vol.5 , pp. 5-17
    • Robson, B.1    Platt, E.2    Fishleigh, R.V.3    Marsden, A.4    Millard, P.5
  • 79
    • 0025317502 scopus 로고
    • Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming
    • Sali, A. & Blundell, T. L. (1990). Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J. Mol. Biol. 212, 403-428.
    • (1990) J. Mol. Biol. , vol.212 , pp. 403-428
    • Sali, A.1    Blundell, T.L.2
  • 80
    • 0025350388 scopus 로고
    • From comparisons of protein sequences and structures to protein modelling and design
    • Sali, A., Overington, J. P., Johnson, M. S. & Blundell, T. L, (1990). From comparisons of protein sequences and structures to protein modelling and design. TIBS, 15, 235-240.
    • (1990) TIBS , vol.15 , pp. 235-240
    • Sali, A.1    Overington, J.P.2    Johnson, M.S.3    Blundell, T.L.4
  • 81
    • 0027401683 scopus 로고
    • Three-dimensional models of four mouse mast cell chymases. Identification of proteoglycan-binding regions and protease-specific antigenic epitopes
    • Sali, A., Matsumoto, R., McNeil, H. P., Karplus, M. & Stevens, R. L. (1993). Three-dimensional models of four mouse mast cell chymases. Identification of proteoglycan-binding regions and protease-specific antigenic epitopes. J. Biol. Chem. 268, 9023-9034.
    • (1993) J. Biol. Chem. , vol.268 , pp. 9023-9034
    • Sali, A.1    Matsumoto, R.2    McNeil, H.P.3    Karplus, M.4    Stevens, R.L.5
  • 82
    • 0025280307 scopus 로고
    • Prediction of homologous protein structures based on conformational searches and energetics
    • Schiffer, O. A., Caldweml, J. W., Kollman, P. A. & Stroud, R. M. (1990). Prediction of homologous protein structures based on conformational searches and energetics. Proteins, 8, 30-43.
    • (1990) Proteins , vol.8 , pp. 30-43
    • Schiffer, O.A.1    Caldweml, J.W.2    Kollman, P.A.3    Stroud, R.M.4
  • 83
  • 84
    • 0024391832 scopus 로고
    • Conformation ofi-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering
    • Sibanda, B. L., Blundell, T. L. & Thornton, I. M. (1989). Conformation ofi-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. J. Mol. Biol. 206, 759-777.
    • (1989) J. Mol. Biol. , vol.206 , pp. 759-777
    • Sibanda, B.L.1    Blundell, T.L.2    Thornton, I.M.3
  • 85
    • 84910894800 scopus 로고
    • SIRIUS. An automated method for the analysis of the preferred packing arrangements between protein groups
    • Singh, J. & Thornton, J. M. (1990). SIRIUS. An automated method for the analysis of the preferred packing arrangements between protein groups. J. Mol. Biol. 17, 195-225.
    • (1990) J. Mol. Biol. , vol.17 , pp. 195-225
    • Singh, J.1    Thornton, J.M.2
  • 86
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
    • Sippl, M. J. (1990). Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol. 213, 859-883.
    • (1990) J. Mol. Biol. , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 87
    • 0026704815 scopus 로고
    • Detection of nativelike models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations
    • Sippl, M. E. & Weitckus, S. (1992). Detection of nativelike models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations. Proteins, 13, 258-271.
    • (1992) Proteins , vol.13 , pp. 258-271
    • Sippl, M.E.1    Weitckus, S.2
  • 88
    • 0027465266 scopus 로고
    • A novel parameterization scheme for energy equations and its use to calculate the structure of protein molecules
    • Snow, M. E. (1993). A novel parameterization scheme for energy equations and its use to calculate the structure of protein molecules. Proteins, 15, 183-193.
    • (1993) Proteins , vol.15 , pp. 183-193
    • Snow, M.E.1
  • 89
    • 0024818499 scopus 로고
    • Stereochemical modeling of disulphide bridges. Criteria for introduction into proteins by site-directed mutagenesis
    • Sowdhamini, R., Srinivasan, N., Shoichet, B., Santi, D. V., Ramakrishnan, C. & Balaram, P. (1989). Stereochemical modeling of disulphide bridges. Criteria for introduction into proteins by site-directed mutagenesis. Protein Eng. 3, 95-103.
    • (1989) Protein Eng , vol.3 , pp. 95-103
    • Sowdhamini, R.1    Srinivasan, N.2    Shoichet, B.3    Santi, D.V.4    Ramakrishnan, C.5    Balaram, P.6
  • 90
    • 0027510701 scopus 로고
    • An automated method for modeling proteins on known templates using distance geometry
    • Srinivasan, S., March, C. J. & Sudarsanam, S. (1993). An automated method for modeling proteins on known templates using distance geometry. Protein Sci. 2, 227-289.
    • (1993) Protein Sci , vol.2 , pp. 227-289
    • Srinivasan, S.1    March, C.J.2    Sudarsanam, S.3
  • 91
    • 15444361103 scopus 로고
    • Prediction of the structure of proteins using related structures, energy minimisation and computer graphics
    • Stewart, D. E., Weiner, P. K. & Wampler, J. E. (1987). Prediction of the structure of proteins using related structures, energy minimisation and computer graphics. J. Mol. Graph. 5, 133-140.
    • (1987) J. Mol. Graph. , vol.5 , pp. 133-140
    • Stewart, D.E.1    Weiner, P.K.2    Wampler, J.E.3
  • 92
    • 0024816521 scopus 로고
    • Construction of side-chains in homology modelling. Application to the C-termina3 lobe of rhizopuspepsin
    • Summers, N. L. & Karplus, M. (1989) Construction of side-chains in homology modelling. Application to the C-termina3 lobe of rhizopuspepsin. J. Mol. Biol. 210, 785-811.
    • (1989) J. Mol. Biol , vol.210 , pp. 785-811
    • Summers, N.L.1    Karplus, M.2
  • 93
    • 0025598934 scopus 로고
    • Modeling of globular proteins. A distance-based search procedure for the construction of insertion/deletion regions and Pro-»non-Pro mutations
    • Summers, N. L. & Karplus, M. (1990). Modeling of globular proteins. A distance-based search procedure for the construction of insertion/deletion regions and Pro-»non-Pro mutations. J. Mol. Biol. 216, 991-1016.
    • (1990) J. Mol. Biol. , vol.216 , pp. 991-1016
    • Summers, N.L.1    Karplus, M.2
  • 94
    • 0023645193 scopus 로고
    • Analysis of side-chain orientations in homologous proteins
    • Summers, N. L., Carson, W. D. & Karplus, M. (1987). Analysis of side-chain orientations in homologous proteins. J. Mol. Biol. 196, 175-198.
    • (1987) J. Mol. Biol. , vol.196 , pp. 175-198
    • Summers, N.L.1    Carson, W.D.2    Karplus, M.3
  • 95
    • 0001433241 scopus 로고
    • Knowledge based modelling of homologous proteins, Part I: Three dimensional frameworks derived from the simultaneous superposition of multiple structures
    • Sutcliffe, M. J., Haneef, I., Carney, D. & Blundell, T. L. (1987a). Knowledge based modelling of homologous proteins, Part I: three dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng. 1, 377-384.
    • (1987) Protein Eng , vol.1 , pp. 377-384
    • Sutcliffe, M.J.1    Haneef, I.2    Carney, D.3    Blundell, T.L.4
  • 96
    • 0000179199 scopus 로고
    • Knowledge based modeling of homologous proteins, Part TT: Rules for the conformation of substituted sidechains
    • Sutcliffe, M. J., Hayes, F. R. F. & Blundell, T. L. (1987). Knowledge based modeling of homologous proteins, Part TT: rules for the conformation of substituted sidechains. Protein Eng. 1, 385-392.
    • (1987) Protein Eng , vol.1 , pp. 385-392
    • Sutcliffe, M.J.1    Hayes, F.R.F.2    Blundell, T.L.3
  • 98
    • 0019881763 scopus 로고
    • Disulphide bridges in globular proteins
    • Thornton, J. M. (1981). Disulphide bridges in globular proteins. J. Mol. Biol. 151, 261-287.
    • (1981) J. Mol. Biol. , vol.151 , pp. 261-287
    • Thornton, J.M.1
  • 101
    • 0027439391 scopus 로고
    • Fragment ranking in modelling of protein structure. Confor ¡nationally constrained environmental amino acid substitution tables
    • Topham, C. M., McLeod, A., Eisenmenger, F., Overington, J. P., Johnson, M. S. & Blundell, T. L. (1993). Fragment ranking in modelling of protein structure. Confor ¡nationally constrained environmental amino acid substitution tables. J. Mol. Biol. 229, 194-220.
    • (1993) J. Mol. Biol , vol.229 , pp. 194-220
    • Topham, C.M.1    McLeod, A.2    Eisenmenger, F.3    Overington, J.P.4    Johnson, M.S.5    Blundell, T.L.6
  • 102
    • 0026696412 scopus 로고
    • Common features of the conformations of antigen-binding loops in immunoglobulins and application to modeling loop conformations
    • Tramontano, A. & Lesk, A. M. (1992). Common features of the conformations of antigen-binding loops in immunoglobulins and application to modeling loop conformations. Proteins, 13, 231-245.
    • (1992) Proteins , vol.13 , pp. 231-245
    • Tramontano, A.1    Lesk, A.M.2
  • 103
    • 0026179489 scopus 로고
    • A new approach to the rapid determination of protein side chain conformations
    • Tuffery, P., Etchebest, C., Hazout, S. & Lavery, R. A. (1991). A new approach to the rapid determination of protein side chain conformations. J. Biomol. Struct. Dynam. 8, 1267-1289.
    • (1991) J. Biomol. Struct. Dynam. , vol.8 , pp. 1267-1289
    • Tuffery, P.1    Etchebest, C.2    Hazout, S.3    Lavery, R.A.4
  • 104
    • 0024395940 scopus 로고
    • A 3-D building blocks approach to analyzing and predicting structure of proteins
    • Unger, R., Harel, D., Wherland, S. & Sussman, J. L. (1989). A 3-D building blocks approach to analyzing and predicting structure of proteins. Proteins, 5, 355-373.
    • (1989) Proteins , vol.5 , pp. 355-373
    • Unger, R.1    Harel, D.2    Wherland, S.3    Sussman, J.L.4
  • 105
    • 0001141858 scopus 로고
    • On the disordered activation domain in trypsinogen. Chemical labelling and low-temperature crystallography
    • Walter, J., Steigemann, W., Singh, T. P., Bartunik, H., Bode, W. & Huber, R. (1982). On the disordered activation domain in trypsinogen. Chemical labelling and low-temperature crystallography. Acta Crystallogr. sect. B, 38, 1462-1472.
    • (1982) Acta Crystallogr. Sect. B , vol.38 , pp. 1462-1472
    • Walter, J.1    Steigemann, W.2    Singh, T.P.3    Bartunik, H.4    Bode, W.5    Huber, R.6
  • 106
    • 0015968881 scopus 로고
    • Computation of structures of homologous proteins: A-lactalbumin from lysozyme
    • Warme, P. K., Momanv, F. A., Rumball, S. V., Tuttle, R. W. & Scheraga, H. A. (1974). Computation of structures of homologous proteins: a-lactalbumin from lysozyme. Biochemistry, 13, 768-782.
    • (1974) Biochemistry , vol.13 , pp. 768-782
    • Warme, P.K.1    Momanv, F.A.2    Rumball, S.V.3    Tuttle, R.W.4    Scheraga, H.A.5
  • 107
    • 0025113022 scopus 로고
    • Turns and their distortions: A proposed new nomenclature
    • Wilmot, C. M. & Thornton, J. M. (1990). Turns and their distortions: a proposed new nomenclature. Protein Eng. 3, 479-493.
    • (1990) Protein Eng , vol.3 , pp. 479-493
    • Wilmot, C.M.1    Thornton, J.M.2
  • 108
    • 0024435638 scopus 로고
    • A computer model to dynamically simulate protein folding: Studies with Cram bin
    • Wilson, C. & Doniach, S. (1989). A computer model to dynamically simulate protein folding: studies with Cram bin. Proteins, 6, 193-209.
    • (1989) Proteins , vol.6 , pp. 193-209
    • Wilson, C.1    Doniach, S.2
  • 109
    • 0027480460 scopus 로고
    • Modeling side-chain conformation for homologous proteins using an energy-based rotamer search
    • Wilson, C., Gregoret, L. M. & Agard, D. A. (1993). Modeling side-chain conformation for homologous proteins using an energy-based rotamer search. J. Mol. Biol. 229, 996-1006.
    • (1993) J. Mol. Biol. , vol.229 , pp. 996-1006
    • Wilson, C.1    Gregoret, L.M.2    Agard, D.A.3
  • 110
    • 0026565850 scopus 로고
    • A variable gap penalty function and feature weights for protein 3-D structure comparisons
    • Zhu, Z.Y., Sali, A. & Blundell, T. L. (1992). A variable gap penalty function and feature weights for protein 3-D structure comparisons. Protein Emj. 5, 43-51.
    • (1992) Protein Emj , vol.5 , pp. 43-51
    • Zhu, Z.Y.1    Sali, A.2    Blundell, T.L.3


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