메뉴 건너뛰기




Volumn 73, Issue 5, 1997, Pages 2359-2375

Does conformational free energy distinguish loop conformations in proteins?

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY;

EID: 0030833061     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(97)78266-3     Document Type: Article
Times cited : (18)

References (67)
  • 1
    • 0026532051 scopus 로고
    • A conformation of cyclosporin A in aqueous environment revealed by the X-ray structure of it cyclosporin-Fab complex
    • Altschuh, D., O. Vix, B. Rees, and J. C. Thierry. 1992. A conformation of cyclosporin A in aqueous environment revealed by the X-ray structure of it cyclosporin-Fab complex, Science. 256:92-94.
    • (1992) Science , vol.256 , pp. 92-94
    • Altschuh, D.1    Vix, O.2    Rees, B.3    Thierry, J.C.4
  • 2
    • 0027299695 scopus 로고
    • Three-dimensional structure of an anti-steroid Fab' and progesterone-Fab' complex
    • Arevalo, J. H., E. A. Stura, M. J. Tausnig, and I. A. Wilson. 1993. Three-dimensional structure of an anti-steroid Fab' and progesterone-Fab' complex. J. Mol. Biol. 231:103-118.
    • (1993) J. Mol. Biol. , vol.231 , pp. 103-118
    • Arevalo, J.H.1    Stura, E.A.2    Tausnig, M.J.3    Wilson, I.A.4
  • 3
    • 33645903407 scopus 로고
    • Solvation thermodynamics of nonionic solutes
    • Ben-Naim, A., and Y, Marcus. 1984. Solvation thermodynamics of nonionic solutes. J. Chem. Phys. 81:2016-2027.
    • (1984) J. Chem. Phys. , vol.81 , pp. 2016-2027
    • Ben-Naim, A.1    Marcus, Y.2
  • 5
    • 0025151612 scopus 로고
    • Small rearrangements in structures of Fv and Fab fragments of antibody D1.3 on antigen binding
    • Bhat, T. N., G. A. Bentley, T. O. Fischmann, G. Boulot, and R. J. Poljak. 1990, Small rearrangements in structures of Fv and Fab fragments of antibody D1.3 on antigen binding. Nature. 347:483-485.
    • (1990) Nature , vol.347 , pp. 483-485
    • Bhat, T.N.1    Bentley, G.A.2    Fischmann, T.O.3    Boulot, G.4    Poljak, R.J.5
  • 6
    • 0029870875 scopus 로고    scopus 로고
    • Crystal structure of the complex of the variable domain of antibody D1.3 and turkey egg white lysozyme: A novel conformational change in antibody CDR-1.3 selects for antigen
    • Braden, B. C., B. A. Fields, X. Ysem, F. A. Goldbaum, W. Dall'Acqua, F. P. Schwarz, R. J. Poljak, and R, A, Mariuzza. 1996. Crystal structure of the complex of the variable domain of antibody D1.3 and turkey egg white lysozyme: a novel conformational change in antibody CDR-1.3 selects for antigen, J. Mol. Biol. 257:889-894.
    • (1996) J. Mol. Biol. , vol.257 , pp. 889-894
    • Braden, B.C.1    Fields, B.A.2    Ysem, X.3    Goldbaum, F.A.4    DalL'Acqua, W.5    Schwarz, F.P.6    Poljak, R.J.7    Mariuzza, R.A.8
  • 7
    • 0023807627 scopus 로고
    • Structure of antibody hypervariable loops reproduced by a conformational search algorithm
    • Bruccoleri, R, E., E. Haber. and J. Novotny. 1988. Structure of antibody hypervariable loops reproduced by a conformational search algorithm. Nature. 335:564-568.
    • (1988) Nature , vol.335 , pp. 564-568
    • Bruccoleri, R.E.1    Haber, E.2    Novotny, J.3
  • 8
    • 0023173201 scopus 로고
    • Prediction of the folding of short polypeptide segments by uniform conformational sampling
    • Bruccoleri, R. E., and M. Karplus. 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
  • 10
    • 0024250301 scopus 로고
    • Polar hydrogen positions in proteins: Empirical energy function placement and neutron diffraction comparison
    • Brünger, A. T., and M. Karplus. 1988. Polar hydrogen positions in proteins: empirical energy function placement and neutron diffraction comparison. Proteins. 4:148-156.
    • (1988) Proteins , vol.4 , pp. 148-156
    • Brünger, A.T.1    Karplus, M.2
  • 11
    • 0027641058 scopus 로고
    • The loop problem in proteins: A Monte Carlo simulated annealing approach
    • Carlacci, L., and S. W. Englander. 1993. The loop problem in proteins: a Monte Carlo simulated annealing approach. Biopolymers. 33: 1271-1286.
    • (1993) Biopolymers , vol.33 , pp. 1271-1286
    • Carlacci, L.1    Englander, S.W.2
  • 12
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia, C., and A. M. Lesk. 1986. The relation between the divergence of sequence and structure in proteins. EMBO J. 5:823-826.
    • (1986) EMBO J. , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 13
    • 0023278330 scopus 로고
    • Canonical structures for the hypervariable regions of immunoglobulins
    • Chothia, C., and A. M. Lesk. 1987. Canonical structures for the hypervariable regions of immunoglobulins, J. Mol. Biol. 196:901-917.
    • (1987) J. Mol. Biol. , vol.196 , pp. 901-917
    • Chothia, C.1    Lesk, A.M.2
  • 14
    • 0019001660 scopus 로고
    • On the prediction of protein structure: The significance of the root-mean-square deviation
    • Cohen, F. E., and M. J. E. Sternberg. 1980. On the prediction of protein structure: the significance of the root-mean-square deviation. J. Mol. Biol. 138:321-333.
    • (1980) J. Mol. Biol. , vol.138 , pp. 321-333
    • Cohen, F.E.1    Sternberg, M.J.E.2
  • 15
    • 0022671293 scopus 로고
    • Modelling of the combining sites of three anti-lysozyme monoclonal antibodies and of the complex between one of the antibodies and its epitope
    • de la Paz, P., B. J. Sutton. M. J. Darsley. and A. R. Rees. 1986. Modelling of the combining sites of three anti-lysozyme monoclonal antibodies and of the complex between one of the antibodies and its epitope. EMBO J. 5:415-425.
    • (1986) EMBO J. , vol.5 , pp. 415-425
    • De la Paz, P.1    Sutton, B.J.2    Darsley, M.J.3    Rees, A.R.4
  • 16
    • 0026589733 scopus 로고
    • The dead-end elimination theorem and its use in protein side-chain positioning
    • Desmet, J., M. De Maeyer, B. Hazes, and I. Lasters. 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
  • 17
    • 0021760092 scopus 로고
    • A comprehensive set of sequence analyses program for the VAX
    • Devereux, J., P. Haeberli, and O. Smithies. 1984. A comprehensive set of sequence analyses program for the VAX. Nucleic Acids Res. 12:387-395.
    • (1984) Nucleic Acids Res. , vol.12 , pp. 387-395
    • Devereux, J.1    Haeberli, P.2    Smithies, O.3
  • 18
    • 0027160197 scopus 로고
    • Backbone-dependent rotomer library for proteins. Application to side-chain prediction
    • Dunbrack, R. L., Jr., and M. Karplus. 1993. Backbone-dependent rotomer library for proteins. Application to side-chain prediction. J. Mol. Biol. 230:543-574.
    • (1993) J. Mol. Biol. , vol.230 , pp. 543-574
    • Dunbrack Jr., R.L.1    Karplus, M.2
  • 19
    • 0027185404 scopus 로고
    • A method to configure protein side-chains from the main-chain trace in homology modelling
    • Eisenmenger, F., P. Argos, and R. Abagyan. 1993. A method to configure protein side-chains from the main-chain trace in homology modelling. J. Mol. Biol. 231:849-860.
    • (1993) J. Mol. Biol. , vol.231 , pp. 849-860
    • Eisenmenger, F.1    Argos, P.2    Abagyan, R.3
  • 20
    • 0016804680 scopus 로고
    • The molecular structure of a dimer composed of the variable portions of the Bence-Jones protein REI refined at 2.0 A resolution
    • Epp, O., E. E. Lattman, M. Schiffer. R. Huber, and W. Palm. 1975. The molecular structure of a dimer composed of the variable portions of the Bence-Jones protein REI refined at 2.0 A resolution, Biochemistry. 14:4943-4952.
    • (1975) Biochemistry , vol.14 , pp. 4943-4952
    • Epp, O.1    Lattman, E.E.2    Schiffer, M.3    Huber, R.4    Palm, W.5
  • 21
    • 0019507195 scopus 로고
    • A hypothetical space-filling model of the V-regions of the galactan-binding myeloma immunoglobulin J539
    • Feldmann, R. J., M. Potter, and C. P. J. Glaudemans. 1981. A hypothetical space-filling model of the V-regions of the galactan-binding myeloma immunoglobulin J539. Mol. Immunol. 18:683-698.
    • (1981) Mol. Immunol. , vol.18 , pp. 683-698
    • Feldmann, R.J.1    Potter, M.2    Glaudemans, C.P.J.3
  • 22
    • 0022842039 scopus 로고
    • Predicting antibody hypervariable loop conformations. II. Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations
    • Fine, R. M., H. Wang. P. S. Shenkin, D. L. Yarmush, and C. Levinthal. 1986. Predicting antibody hypervariable loop conformations. II. Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations. Proteins. 1:342-362.
    • (1986) Proteins , vol.1 , pp. 342-362
    • Fine, R.M.1    Wang, H.2    Shenkin, P.S.3    Yarmush, D.L.4    Levinthal, C.5
  • 24
    • 0021095485 scopus 로고
    • Structure of a novel Bence-Jones protein (Rhe) fragment at 1.6 Å resolution
    • Furey, W., Jr., B. C. Wang, C. S. Yoo, and M. Sax. 1983. Structure of a novel Bence-Jones protein (Rhe) fragment at 1.6 Å resolution. J. Mol. Biol. 167:661-692.
    • (1983) J. Mol. Biol. , vol.167 , pp. 661-692
    • Furey Jr., W.1    Wang, B.C.2    Yoo, C.S.3    Sax, M.4
  • 25
    • 0023779259 scopus 로고
    • Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
    • Gilson, M. K., and B. Honig. 1988. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins. 4:7-18.
    • (1988) Proteins , vol.4 , pp. 7-18
    • Gilson, M.K.1    Honig, B.2
  • 26
    • 0024329804 scopus 로고
    • Three-dimensional structure of a fluorescein-fab complex crystallized in 2-methyl-2.4-pcntanediol
    • Herren, J. N., X.-M. He, M. L., Mason, E. W. Voss, Jr., and A. B. Edmundson. 1989. Three-dimensional structure of a fluorescein-fab complex crystallized in 2-methyl-2.4-pcntanediol. Proteins. 5:271-280.
    • (1989) Proteins , vol.5 , pp. 271-280
    • Herren, J.N.1    He, X.-M.2    Mason, M.L.3    Voss Jr., E.W.4    Edmundson, A.B.5
  • 27
    • 33751385054 scopus 로고
    • Macroscopic models of aqueous solutions: Biological and chemical applications
    • Honig, B., K. Sharp, and A.-S. Yang. 1993. Macroscopic models of aqueous solutions: biological and chemical applications. J. Phys. Chem. 97:1101-1109.
    • (1993) J. Phys. Chem. , vol.97 , pp. 1101-1109
    • Honig, B.1    Sharp, K.2    Yang, A.-S.3
  • 28
    • 0000338489 scopus 로고
    • Comparison of solventinaccessible cores of homologous proteins: Definitions useful for protein modelling
    • Hubbard, T. J. P., and T. L. Blundell. 1987. Comparison of solventinaccessible cores of homologous proteins: definitions useful for protein modelling. Protein Eng. 1:159-171.
    • (1987) Protein Eng. , vol.1 , pp. 159-171
    • Hubbard, T.J.P.1    Blundell, T.L.2
  • 29
    • 85022423714 scopus 로고
    • Electrostatic contributions to solvation energies: Comparison of free energy perturbation and continuum calculations
    • Jean-Charles, A., A. Nicholls, K. Sharp, B. Honig, A. Tempezyk, T. F. Hendrickson, and W. C. Still. 1991. Electrostatic contributions to solvation energies: comparison of free energy perturbation and continuum calculations. J. Am. Chem. Soc. 113:1454-1455.
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 1454-1455
    • Jean-Charles, A.1    Nicholls, A.2    Sharp, K.3    Honig, B.4    Tempezyk, A.5    Hendrickson, T.F.6    Still, W.C.7
  • 30
    • 0022701772 scopus 로고
    • Using known substructures in protein model building and crystallography
    • Jones, T. A., and S. Thirup. 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.A.1    Thirup, S.2
  • 31
    • 0017747498 scopus 로고
    • Unusual distributions of amino acids in complementarity-determining (hypervariable) segments of heavy and light chains of immunoglobulins and their possible roles in specificity of antibody-combining sites
    • Kabat, E. A., T. T. Wu, and H. Bilofsky. 1977. Unusual distributions of amino acids in complementarity-determining (hypervariable) segments of heavy and light chains of immunoglobulins and their possible roles in specificity of antibody-combining sites. J. Biol. Chem. 252:6609-6616.
    • (1977) J. Biol. Chem. , vol.252 , pp. 6609-6616
    • Kabat, E.A.1    Wu, T.T.2    Bilofsky, H.3
  • 33
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W., and C. Sander. 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
  • 34
    • 0028343413 scopus 로고
    • Application of a self-consistent mean field theory to predict side-chains conformation and estimate their conformational entropy
    • Koehl, P., and M. Uelarue. 1994. Application of a self-consistent mean field theory to predict 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    Uelarue, M.2
  • 35
    • 0029565303 scopus 로고
    • A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modeling
    • Koehl, P., and M. Delarue. 1995. A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modeling. Nature Struct. Biol. 2:163-170.
    • (1995) Nature Struct. Biol. , vol.2 , pp. 163-170
    • Koehl, P.1    Delarue, M.2
  • 36
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis, P. J. 1991. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-950.
    • (1991) J. Appl. Crystallogr , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 37
    • 0026687920 scopus 로고
    • Three-dimensional structure of two crystal forms of FabR19.9 from a monoclonal anti-arsonate antibody
    • Lacombe, M.-B., P. M. Alzari, R. J. Poljak, and A. Nisonoff. 1992. Three-dimensional structure of two crystal forms of FabR19.9 from a monoclonal anti-arsonate antibody. Proc. Natl. Acad. Sci. USA. 89: 9429-9433.
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 9429-9433
    • Lacombe, M.-B.1    Alzari, P.M.2    Poljak, R.J.3    Nisonoff, A.4
  • 38
    • 0027493639 scopus 로고
    • The fuzzy-end elimination theorem: Correctly implementing the side-chain placement algorithm based on the dead-end elimination theorem
    • Lasters, I., and J. Desmet. 1993. The fuzzy-end elimination theorem: correctly implementing the side-chain placement algorithm based on the dead-end elimination theorem. Protein Eng. 6:717-722.
    • (1993) Protein Eng. , vol.6 , pp. 717-722
    • Lasters, I.1    Desmet, J.2
  • 39
    • 0026019108 scopus 로고
    • Prediction of protein side-chain conformation by packing optimisation
    • Lee. C., and S. Subbiah. 1991. Prediction of protein side-chain conformation by packing optimisation. J. Mol. Biol. 217:373-388.
    • (1991) J. Mol. Biol. , vol.217 , pp. 373-388
    • Lee, C.1    Subbiah, S.2
  • 40
    • 0021154278 scopus 로고
    • A refined model for the variable domains (Fv) of the J539 β(1.6)-D-galactan-binding immunoglobulin
    • Mainhart, C. R., M. Potter, and R. J. Feldmann. 1984. A refined model for the variable domains (Fv) of the J539 β(1.6)-D-galactan-binding immunoglobulin. Mol. Immunol. 21:469-478.
    • (1984) Mol. Immunol , vol.21 , pp. 469-478
    • Mainhart, C.R.1    Potter, M.2    Feldmann, R.J.3
  • 41
    • 0028012138 scopus 로고
    • Significance of root-meansquare deviation in comparing three-dimensional structures of globular proteins
    • Maiorov, V. N., and G. M. Grippen. 1994. Significance of root-meansquare deviation in comparing three-dimensional structures of globular proteins. J. Mol. Biol. 235:625-634.
    • (1994) J. Mol. Biol , vol.235 , pp. 625-634
    • Maiorov, V.N.1    Grippen, G.M.2
  • 42
    • 0019119230 scopus 로고
    • Crystallographic refinement and atomic models of the intact immunoglobulin molecule Kol and its antigen-binding fragment at 3.0 Å and 1.9 Å resolution
    • Marquart, M., J. Deisenhofer, and R. Huber. 1980. Crystallographic refinement and atomic models of the intact immunoglobulin molecule Kol and its antigen-binding fragment at 3.0 Å and 1.9 Å resolution. J. Mol. Biol. 141:369-391.
    • (1980) J. Mol. Biol. , vol.141 , pp. 369-391
    • Marquart, M.1    Deisenhofer, J.2    Huber, R.3
  • 43
    • 0024310232 scopus 로고
    • Modeling antibody hypervariable loops: A combined algorithm
    • Martin, A. C. R., J. C. Cheetham, and A. R. Rees. 1989. Modeling antibody hypervariable loops: a combined algorithm. Proc. Natl. Acad. Sci. USA. 86:9268-9272.
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 9268-9272
    • Martin, A.C.R.1    Cheetham, J.C.2    Rees, A.R.3
  • 44
    • 0022788691 scopus 로고
    • An algorithm for determining the conformation of polypeptide segments in proteins by systematic search
    • Moult, J., and M. N. G. James. 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
  • 45
    • 84986486656 scopus 로고
    • A rapid finite difference algorithm utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
    • Nicholls, A., and B. Honig. 1991. A rapid finite difference algorithm utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J. Comp. Chem. 12:435-445.
    • (1991) J. Comp. Chem , vol.12 , pp. 435-445
    • Nicholls, A.1    Honig, B.2
  • 46
    • 0022032207 scopus 로고
    • On the specificity of antibody/antigen interactions: Phosphocholine binding to McPC603 and the correlation of three-dimensional structure and sequence data
    • Padlan, E. A., G. H. Cohen, and D. R. Davics. 1985. On the specificity of antibody/antigen interactions: phosphocholine binding to McPC603 and the correlation of three-dimensional structure and sequence data. Ann. Inst. Pasteur. 136C:271-276.
    • (1985) Ann. Inst. Pasteur , vol.136 C , pp. 271-276
    • Padlan, E.A.1    Cohen, G.H.2    Davics, D.R.3
  • 47
    • 0343055582 scopus 로고
    • Structure of an antibody-antigen complex: Crystal structure of the HyHEL-10 Fab-lysozyme complex
    • Padlan, E., A.. E. W. Silverton, S. Sheriff, and G. H. Cohen. 1989. Structure of an antibody-antigen complex: crystal structure of the HyHEL-10 Fab-lysozyme complex. Proc. Natl. Acad. Sci. USA. 86:5938-5942.
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 5938-5942
    • Padlan, E.1    Silverton, A.E.W.2    Sheriff, S.3    Cohen, G.H.4
  • 48
    • 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 F. M. Richards. 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
  • 49
    • 0024290488 scopus 로고
    • Helix signals in proteins
    • Presta, L. G., and G. D. Rose. 1988. Helix signals in proteins. Science. 240:1632-1641.
    • (1988) Science , vol.240 , pp. 1632-1641
    • Presta, L.G.1    Rose, G.D.2
  • 50
    • 0015834475 scopus 로고
    • Comparison of super-secondary structures in proteins
    • Rao, S. T., and M. G. Rossmann. 1973. Comparison of super-secondary structures in proteins. J. Mol. Biol. 76:241-256.
    • (1973) J. Mol. Biol. , vol.76 , pp. 241-256
    • Rao, S.T.1    Rossmann, M.G.2
  • 51
    • 0019325435 scopus 로고
    • A systematic approach to the comparison of protein structures
    • Remington, S. J., and B. W. Matthews. 1980. A systematic approach to the comparison of protein structures. J. Mol. Biol. 140:77-99.
    • (1980) J. Mol. Biol. , vol.140 , pp. 77-99
    • Remington, S.J.1    Matthews, B.W.2
  • 52
    • 0026530262 scopus 로고
    • Taxonomy and conformational analysis of loops in proteins
    • Ring, C. S., D. G. Kneller, R. Langridge, and F. E. Cohen. 1992. Taxonomy and conformational analysis of loops in proteins. J. Mol. Biol. 224:685-699.
    • (1992) J. Mol. Biol. , vol.224 , pp. 685-699
    • Ring, C.S.1    Kneller, D.G.2    Langridge, R.3    Cohen, F.E.4
  • 53
    • 0026587998 scopus 로고
    • Structural evidence for induced fit as a mechanism for antibody-antigen recognition
    • Rini, J. M., U. Schulze-Gahmen, and I. A. Wilson. 1992. Structural evidence for induced fit as a mechanism for antibody-antigen recognition. Science. 255:959-965.
    • (1992) Science , vol.255 , pp. 959-965
    • Rini, J.M.1    Schulze-Gahmen, U.2    Wilson, I.A.3
  • 54
    • 36449006131 scopus 로고
    • Modelling side-chains in peptides and proteins: Application of the locally enhanced sampling and the simulated annealing method to find minimum energy conformations
    • Roitberg, A., and R. Elber. 1991. Modelling side-chains in peptides and proteins: application of the locally enhanced sampling and the simulated annealing method to find minimum energy conformations. J. Chem. Phys. 95:9277-9287.
    • (1991) J. Chem. Phys. , vol.95 , pp. 9277-9287
    • Roitberg, A.1    Elber, R.2
  • 55
    • 0017855552 scopus 로고
    • Preliminary refinement and structural analysis of the Fab fragment from human immunoglobulin New at 2.0 Å resolution
    • Saul, F. A., L. M. Amzel, and R. J. Poljak. 1978. Preliminary refinement and structural analysis of the Fab fragment from human immunoglobulin New at 2.0 Å resolution. J. Biol. Chem. 253:585-597.
    • (1978) J. Biol. Chem , vol.253 , pp. 585-597
    • Saul, F.A.1    Amzel, L.M.2    Poljak, R.J.3
  • 56
    • 0023478807 scopus 로고
    • Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures
    • Shenkin, P. S., D. L. Yarmush, R. M. Fine. H. Wang, and C. Levinthal. 1987. Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures. Biopolymers. 26:2053-2085.
    • (1987) Biopolymers , vol.26 , pp. 2053-2085
    • Shenkin, P.S.1    Yarmush, D.L.2    Fine, R.M.3    Wang, H.4    Levinthal, C.5
  • 58
    • 32844457567 scopus 로고
    • Accurate calculation of hydration free energies using macroscopic solvent models
    • Sitkoff, D., K. A. Sharp, and B. Honig. 1994. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98:1978-1988.
    • (1994) J. Phys. Chem , vol.98 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 59
    • 0028040064 scopus 로고
    • Evaluation of the conformational free energies of loops in proteins
    • Smith, K. C., and B. Honig. 1994. Evaluation of the conformational free energies of loops in proteins. Proteins. 18:119-132.
    • (1994) Proteins , vol.18 , pp. 119-132
    • Smith, K.C.1    Honig, B.2
  • 60
    • 0000328844 scopus 로고
    • A new vertex algorithm to calculate solvent accessible surface areas
    • Sridharan, S., A. Nicholls, and B. Honig. 1992. A new vertex algorithm to calculate solvent accessible surface areas. Biophys. J. 61:A174.
    • (1992) Biophys. J. , vol.61
    • Sridharan, S.1    Nicholls, A.2    Honig, B.3
  • 61
    • 0025321903 scopus 로고
    • Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 Å
    • Stanfield, R. L., T. M. Fieser, R. A. Lerner, and I. A. Wilson. 1990. Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 Å. Science. 248:712-719.
    • (1990) Science , vol.248 , pp. 712-719
    • Stanfield, R.L.1    Fieser, T.M.2    Lerner, R.A.3    Wilson, I.A.4
  • 62
    • 0025744379 scopus 로고
    • Three-dimensional structure of murine anti-pazophenylarsonate Fab 36-71. 1. X-ray crystallography, site-directed mutagenesis, and modeling of the complex with hapten
    • Strong, R. K., R. Campbell, D. R. Rose, G. A. Petsko, J. Sharon, and M. N. Margolies. 1991. Three-dimensional structure of murine anti-pazophenylarsonate Fab 36-71. 1. X-ray crystallography, site-directed mutagenesis, and modeling of the complex with hapten. Biochemistry. 30:3739-3748.
    • (1991) Biochemistry , vol.30 , pp. 3739-3748
    • Strong, R.K.1    Campbell, R.2    Rose, D.R.3    Petsko, G.A.4    Sharon, J.5    Margolies, M.N.6
  • 63
    • 0025598934 scopus 로고
    • Modeling of globular proteins. A distance-based data search procedure for the construction of insertion/deletion regions and Pro↔non-Pro mutations
    • Summers, N. L., and M. Karplus. 1990. Modeling of globular proteins. A distance-based data 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
  • 64
    • 0026696412 scopus 로고
    • Common features of the conformations of antigen-binding loops in immunoglobulins and application to modelling loop conformations
    • Tramontano, A., and A. M. Lesk. 1992. Common features of the conformations of antigen-binding loops in immunoglobulins and application to modelling loop conformations. Proteins. 13:231-245.
    • (1992) Proteins , vol.13 , pp. 231-245
    • Tramontano, A.1    Lesk, A.M.2
  • 65
    • 0026179489 scopus 로고
    • A new approach to the rapid determination of protein side chain conformations
    • Tuffery, P., C. Etchebest, S. Hazout, and R. Lavery. 1991. A new approach to the rapid determination of protein side chain conformations. J. Biomol. Struct. Dyn. 8:1267-1289.
    • (1991) J. Biomol. Struct. Dyn. , vol.8 , pp. 1267-1289
    • Tuffery, P.1    Etchebest, C.2    Hazout, S.3    Lavery, R.4
  • 66
    • 0027462844 scopus 로고
    • Crystallographic analysis of the interaction between cyclosporin A and the Fab fragment of a monoclonal antibody
    • Vix, O., B. Rees, J.-C. Thierry, and D. Altschuh. 1993. Crystallographic analysis of the interaction between cyclosporin A and the Fab fragment of a monoclonal antibody. Proteins. 15:339-348.
    • (1993) Proteins , vol.15 , pp. 339-348
    • Vix, O.1    Rees, B.2    Thierry, J.-C.3    Altschuh, D.4
  • 67
    • 0027480460 scopus 로고
    • Modeling side-chain conformation for homologous proteins using an energy-based rotamer search
    • Wilson, C., L. M. Gregoret, and D. A. Agard. 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.