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Volumn 72, Issue 2, 1999, Pages 135-155

Annealing in crystallography: A powerful optimization tool

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PROTEIN;

EID: 0032847732     PISSN: 00796107     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0079-6107(99)00004-8     Document Type: Article
Times cited : (23)

References (90)
  • 1
    • 0026681839 scopus 로고
    • Optimal protocol and trajectory visualization for conformational searches of peptides and proteins
    • Abagyan R., Argos P. Optimal protocol and trajectory visualization for conformational searches of peptides and proteins. J. Mol. Biol. 225:1992;519-532.
    • (1992) J. Mol. Biol. , vol.225 , pp. 519-532
    • Abagyan, R.1    Argos, P.2
  • 3
    • 0030986177 scopus 로고    scopus 로고
    • Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement
    • Adams P.D., Pannu N.S., Read R.J., Brunger A.T. Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement. Proc. Natl. Acad. Sci. USA. 94:1997;5018-5023.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 5018-5023
    • Adams, P.D.1    Pannu, N.S.2    Read, R.J.3    Brunger, A.T.4
  • 4
    • 0032942076 scopus 로고    scopus 로고
    • Extending the limits of molecular replacement through combined simulated annealing and maximum likelihood refinement
    • Adams P.D., Pannu N.S., Read R.J., Brunger A.T. Extending the limits of molecular replacement through combined simulated annealing and maximum likelihood refinement. Acta Cryst. D. 55:1999;181-190.
    • (1999) Acta Cryst. D , vol.55 , pp. 181-190
    • Adams, P.D.1    Pannu, N.S.2    Read, R.J.3    Brunger, A.T.4
  • 5
    • 11644328584 scopus 로고
    • Systematic analysis of structural data as a research technique in organic chemistry
    • Allen F.H., Kennard O., Taylor R. Systematic analysis of structural data as a research technique in organic chemistry. Acc. Chem. Res. 16:1983;146-153.
    • (1983) Acc. Chem. Res. , vol.16 , pp. 146-153
    • Allen, F.H.1    Kennard, O.2    Taylor, R.3
  • 6
    • 84950199216 scopus 로고
    • A recursive formulation for constrained mechanical system dynamics. I. Open loop systems
    • Bae D.-S., Haug E.J. A recursive formulation for constrained mechanical system dynamics. I. Open loop systems. Mech. Struct. Mach. 15:1987;359-382.
    • (1987) Mech. Struct. Mach. , vol.15 , pp. 359-382
    • Bae, D.-S.1    Haug, E.J.2
  • 7
    • 84941502604 scopus 로고
    • A recursive formulation for constrained mechanical system dynamics. II. Open loop systems
    • Bae D.-S., Haug E.J. A recursive formulation for constrained mechanical system dynamics. II. Open loop systems. Mech. Struct. Mach. 15:1988;481-506.
    • (1988) Mech. Struct. Mach. , vol.15 , pp. 481-506
    • Bae, D.-S.1    Haug, E.J.2
  • 9
    • 0029022355 scopus 로고
    • Conformational variability of solution nuclear magnetic resonance structures
    • Bonvin A.M.J.J., Brunger A.T. Conformational variability of solution nuclear magnetic resonance structures. J. Mol. Biol. 250:1995;80-93.
    • (1995) J. Mol. Biol. , vol.250 , pp. 80-93
    • Bonvin, A.M.J.J.1    Brunger, A.T.2
  • 10
    • 0029693351 scopus 로고    scopus 로고
    • Do NOE distances contain enough information to assess the relative populations of multi-conformer structures?
    • Bonvin A.M.J.J., Brunger A.T. Do NOE distances contain enough information to assess the relative populations of multi-conformer structures? J. Biomol. NMR. 7:1996;72-76.
    • (1996) J. Biomol. NMR , vol.7 , pp. 72-76
    • Bonvin, A.M.J.J.1    Brunger, A.T.2
  • 11
    • 0023339433 scopus 로고
    • Distance geometry and related methods for protein structure determination from NMR data
    • Braun W. Distance geometry and related methods for protein structure determination from NMR data. Q. Rev. Biophys. 19:1987;115-157.
    • (1987) Q. Rev. Biophys. , vol.19 , pp. 115-157
    • Braun, W.1
  • 12
    • 0022336792 scopus 로고
    • Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm
    • Braun W., Go N. Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm. J. Mol. Biol. 186:1985;611-626.
    • (1985) J. Mol. Biol. , vol.186 , pp. 611-626
    • Braun, W.1    Go, N.2
  • 13
    • 0000801550 scopus 로고
    • A multisolution method of phase determination by combined maximization of entropy and likelihood. III. Extension to powder diffraction data
    • Bricogne G. A multisolution method of phase determination by combined maximization of entropy and likelihood. III. Extension to powder diffraction data. Acta Cryst. A. 47:1991;803-829.
    • (1991) Acta Cryst. a , vol.47 , pp. 803-829
    • Bricogne, G.1
  • 14
    • 0001936036 scopus 로고
    • Direct phase determination by entropy maximization and likelihood ranking: Status report and perspectives
    • Bricogne G. Direct phase determination by entropy maximization and likelihood ranking: status report and perspectives. Acta Cryst. D. 49:1993;37-60.
    • (1993) Acta Cryst. D , vol.49 , pp. 37-60
    • Bricogne, G.1
  • 15
    • 0031059040 scopus 로고    scopus 로고
    • Bayesian statistical viewpoint on structure determination: Basic concepts and examples
    • Bricogne G. Bayesian statistical viewpoint on structure determination: basic concepts and examples. Meth. Enzy. 276:1997;361-423.
    • (1997) Meth. Enzy. , vol.276 , pp. 361-423
    • Bricogne, G.1
  • 16
    • 0024279342 scopus 로고
    • Crystallographic refinement by simulated annealing: Application to a 2.8 Å resolution structure of aspartate aminotransferase
    • Brunger A.T. Crystallographic refinement by simulated annealing: application to a 2.8 Å resolution structure of aspartate aminotransferase. J. Mol. Biol. 203:1988;803-816.
    • (1988) J. Mol. Biol. , vol.203 , pp. 803-816
    • Brunger, A.T.1
  • 17
    • 0026597444 scopus 로고
    • The free R value: A novel statistical quantity for assessing the accuracy of crystal structures
    • Brunger A.T. The free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature. 355:1992;472-474.
    • (1992) Nature , vol.355 , pp. 472-474
    • Brunger, A.T.1
  • 18
    • 0000870109 scopus 로고
    • Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: Application to crambin
    • Brunger A.T., Clore G.M., Gronenborn A.M., Karplus M. Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. Proc. Natl. Acad. Sci. USA. 83:1986;3801-3805.
    • (1986) Proc. Natl. Acad. Sci. USA , vol.83 , pp. 3801-3805
    • Brunger, A.T.1    Clore, G.M.2    Gronenborn, A.M.3    Karplus, M.4
  • 19
    • 0023140814 scopus 로고
    • Crystallographic R factor refinement by molecular dynamics
    • Brunger A.T., Kuriyan J., Karplus M. Crystallographic R factor refinement by molecular dynamics. Science. 235:1987;458-460.
    • (1987) Science , vol.235 , pp. 458-460
    • Brunger, A.T.1    Kuriyan, J.2    Karplus, M.3
  • 20
    • 0002208132 scopus 로고
    • Crystallographic refinement by simulated annealing: Application to a 1.5 Å resolution structure of crambin
    • Brunger A.T., Karplus M., Petsko G.A. Crystallographic refinement by simulated annealing: application to a 1.5 Å resolution structure of crambin. Acta Cryst. A. 45:1989;50-61.
    • (1989) Acta Cryst. a , vol.45 , pp. 50-61
    • Brunger, A.T.1    Karplus, M.2    Petsko, G.A.3
  • 21
    • 84901961522 scopus 로고
    • Slow-cooling protocols for crystallographic refinement by simulated annealing
    • Brunger A.T., Krukowski A., Erickson J. Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Cryst. A. 46:1990;585-593.
    • (1990) Acta Cryst. a , vol.46 , pp. 585-593
    • Brunger, A.T.1    Krukowski, A.2    Erickson, J.3
  • 22
    • 0027918891 scopus 로고
    • Assessment of the quality of solution nuclear magnetic resonance structures by complete cross-validation
    • Brunger A.T., Clore G.M., Gronenborn A.M., Saffrich R., Nilges M. Assessment of the quality of solution nuclear magnetic resonance structures by complete cross-validation. Science. 261:1993;328-331.
    • (1993) Science , vol.261 , pp. 328-331
    • Brunger, A.T.1    Clore, G.M.2    Gronenborn, A.M.3    Saffrich, R.4    Nilges, M.5
  • 23
    • 85005537029 scopus 로고
    • Thermal motion and conformational disorder in protein crystal structures: Comparison of multi-conformer and time-averaging models
    • Burling F.T., Brunger A.T. Thermal motion and conformational disorder in protein crystal structures: comparison of multi-conformer and time-averaging models. Israel J. Chem. 34:1994;165-175.
    • (1994) Israel J. Chem. , vol.34 , pp. 165-175
    • Burling, F.T.1    Brunger, A.T.2
  • 24
    • 0030038545 scopus 로고    scopus 로고
    • Direct observation of protein solvation and discrete disorder with experimental crystallographic phases
    • Burling F.T., Weis W.I., Flaherty K.M., Brunger A.T. Direct observation of protein solvation and discrete disorder with experimental crystallographic phases. Science. 271:1996;72-77.
    • (1996) Science , vol.271 , pp. 72-77
    • Burling, F.T.1    Weis, W.I.2    Flaherty, K.M.3    Brunger, A.T.4
  • 25
    • 0000939457 scopus 로고
    • The three-dimensional structure of a-purothionin in solution: Combined use of nuclear magnetic resonance, distance geometry and restrained molecular dynamics
    • Clore G.M., Nilges M., Sukumaran D.K., Brunger A.T., Karplus M., Gronenborn A.M. The three-dimensional structure of a-purothionin in solution: combined use of nuclear magnetic resonance, distance geometry and restrained molecular dynamics. EMBO J. 5:1986;2729-2735.
    • (1986) EMBO J. , vol.5 , pp. 2729-2735
    • Clore, G.M.1    Nilges, M.2    Sukumaran, D.K.3    Brunger, A.T.4    Karplus, M.5    Gronenborn, A.M.6
  • 26
    • 0024300819 scopus 로고
    • Refinement of the solution structure of the DNA dodecamer 5′d(CGCGPATTCGCG)2 containing a stable purine-thymine base pair: Combined use of nuclear magnetic resonance and restrained molecular dynamics
    • Clore G.M., Oschkinat H., McLaughlin L.W., Benseler F., Scalfi-Happ C., Happ E., Gronenborn A.M. Refinement of the solution structure of the DNA dodecamer 5′d(CGCGPATTCGCG)2 containing a stable purine-thymine base pair: combined use of nuclear magnetic resonance and restrained molecular dynamics. Biochemistry. 27:1988;4185-4197.
    • (1988) Biochemistry , vol.27 , pp. 4185-4197
    • Clore, G.M.1    Oschkinat, H.2    McLaughlin, L.W.3    Benseler, F.4    Scalfi-Happ, C.5    Happ, E.6    Gronenborn, A.M.7
  • 27
    • 0003235926 scopus 로고
    • Computer simulation of multiple chain systems - The effect of density on the average chain dimension
    • Curro J. Computer simulation of multiple chain systems - the effect of density on the average chain dimension. J. Chem. Phys. 61:1974;1203-1207.
    • (1974) J. Chem. Phys. , vol.61 , pp. 1203-1207
    • Curro, J.1
  • 29
    • 0000651098 scopus 로고
    • A real-space refinement procedure for proteins
    • Diamond R. A real-space refinement procedure for proteins. Acta Cryst. A. 27:1971;436-452.
    • (1971) Acta Cryst. a , vol.27 , pp. 436-452
    • Diamond, R.1
  • 30
    • 79952608525 scopus 로고
    • Accurate bond and angle parameters for X-ray structure refinement
    • Engh R.A., Huber R. Accurate bond and angle parameters for X-ray structure refinement. Acta Cryst. A. 47:1991;392-400.
    • (1991) Acta Cryst. a , vol.47 , pp. 392-400
    • Engh, R.A.1    Huber, R.2
  • 31
    • 0009550579 scopus 로고
    • Testing the method of crystallographic refinement using molecular dynamics
    • Fujinaga M., Gros P., van Gunsteren W.F. Testing the method of crystallographic refinement using molecular dynamics. J. Appl. Cryst. 22:1989;1-8.
    • (1989) J. Appl. Cryst. , vol.22 , pp. 1-8
    • Fujinaga, M.1    Gros, P.2    Van Gunsteren, W.F.3
  • 32
    • 0028432974 scopus 로고
    • The impact of direct refinement against three-bond HN-C alpha H coupling constants on protein structure determination by NMR
    • Garrett D.S., Kuszewski J., Hancock T.J., Lodi P.J., Vuister G W., Gronenborn A.M., Clore G.M. The impact of direct refinement against three-bond HN-C alpha H coupling constants on protein structure determination by NMR. J. Magn. Res. B. 104:1994;99-103.
    • (1994) J. Magn. Res. B , vol.104 , pp. 99-103
    • Garrett, D.S.1    Kuszewski, J.2    Hancock, T.J.3    Lodi, P.J.4    Vuister, G.W.5    Gronenborn, A.M.6    Clore, G.M.7
  • 34
    • 0025173665 scopus 로고
    • Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics
    • Gros P., van Gunsteren W.F., Hol W.G.J. Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics. Science. 249:1990;1149-1152.
    • (1990) Science , vol.249 , pp. 1149-1152
    • Gros, P.1    Van Gunsteren, W.F.2    Hol, W.G.J.3
  • 35
    • 0022333121 scopus 로고
    • Stereochemically restrained refinement of macromolecular structures
    • Hendrickson W.A. Stereochemically restrained refinement of macromolecular structures. Meth. Enzymol. 115:1985;252-270.
    • (1985) Meth. Enzymol. , vol.115 , pp. 252-270
    • Hendrickson, W.A.1
  • 36
    • 0026095584 scopus 로고
    • Determination of macromolecular structures from anomalous diffraction of synchrotron radiation
    • Hendrickson W.A. Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science. 254:1991;51-58.
    • (1991) Science , vol.254 , pp. 51-58
    • Hendrickson, W.A.1
  • 37
    • 0000443232 scopus 로고
    • Die Faltmolekülmethode - eine neue Methode zur Bestimmung der Kristallstruktur bei Ganz oder Teilweise bekannter Molekülstruktur
    • Hoppe W. Die Faltmolekülmethode - eine neue Methode zur Bestimmung der Kristallstruktur bei Ganz oder Teilweise bekannter Molekülstruktur. Acta Cryst. 10:1957;750-751.
    • (1957) Acta Cryst. , vol.10 , pp. 750-751
    • Hoppe, W.1
  • 38
    • 0017581877 scopus 로고
    • Penicillopepsin from Penicillium janthinellum crystal structure at 2.8 Å and sequence homology with porcine pepsin
    • Hsu I.N., Delbaere L.T.J., James M.N.G., Hoffman T. Penicillopepsin from Penicillium janthinellum crystal structure at 2.8 Å and sequence homology with porcine pepsin. Nature. 266:1977;140-145.
    • (1977) Nature , vol.266 , pp. 140-145
    • Hsu, I.N.1    Delbaere, L.T.J.2    James, M.N.G.3    Hoffman, T.4
  • 39
    • 0000040038 scopus 로고
    • A fast recursive algorithm for molecular dynamics simulation
    • Jain A., Vaidehi N., Rodriguez G. A fast recursive algorithm for molecular dynamics simulation. J. Comp. Phys. 106:1983;258-268.
    • (1983) J. Comp. Phys. , vol.106 , pp. 258-268
    • Jain, A.1    Vaidehi, N.2    Rodriguez, G.3
  • 40
    • 84889120137 scopus 로고
    • Improved methods for building protein models in electron density maps and the location of errors in these models
    • Jones T.A., Zou J.Y., Cowan S.W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst. A. 47:1991;110-119.
    • (1991) Acta Cryst. a , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 42
    • 12244297937 scopus 로고
    • Vicinal proton coupling in nuclear magnetic resonance
    • Karplus M. Vicinal proton coupling in nuclear magnetic resonance. J. Am. Chem. Soc. 85:1963;2870-2871.
    • (1963) J. Am. Chem. Soc. , vol.85 , pp. 2870-2871
    • Karplus, M.1
  • 43
    • 0025048105 scopus 로고
    • Molecular dynamics simulations in biology
    • Karplus M., Petsko G.A. Molecular dynamics simulations in biology. Nature. 347:1990;631-639.
    • (1990) Nature , vol.347 , pp. 631-639
    • Karplus, M.1    Petsko, G.A.2
  • 44
    • 0025613125 scopus 로고
    • Refinement of the NMR structures for acyl carrier protein with scalar coupling data
    • Kim Y., Prestegard J.H. Refinement of the NMR structures for acyl carrier protein with scalar coupling data. Proteins Structure Function Genetics. 8:1990;377-385.
    • (1990) Proteins Structure Function Genetics , vol.8 , pp. 377-385
    • Kim, Y.1    Prestegard, J.H.2
  • 46
    • 0030586823 scopus 로고    scopus 로고
    • Cross-validation in crystallography: Practice and applications
    • Kleywegt G.J., Brunger A.T. Cross-validation in crystallography: practice and applications. Structure. 4:1996;897-904.
    • (1996) Structure , vol.4 , pp. 897-904
    • Kleywegt, G.J.1    Brunger, A.T.2
  • 47
    • 0023053635 scopus 로고
    • Effect of anisotropy and anharmonicity on protein crystallographic refinement
    • Kuriyan J., Petsko G.A., Levy R.M., Karplus M. Effect of anisotropy and anharmonicity on protein crystallographic refinement. J. Mol. Biol. 190:1986;227-254.
    • (1986) J. Mol. Biol. , vol.190 , pp. 227-254
    • Kuriyan, J.1    Petsko, G.A.2    Levy, R.M.3    Karplus, M.4
  • 49
    • 0029314335 scopus 로고
    • The impact of direct refinement against proton chemical shifts on protein structure determination by NMR
    • Kuszewski J., Gronenborn A.M., Clore G.M. The impact of direct refinement against proton chemical shifts on protein structure determination by NMR. J. Magn. Res. B. 107:1995;293-297.
    • (1995) J. Magn. Res. B , vol.107 , pp. 293-297
    • Kuszewski, J.1    Gronenborn, A.M.2    Clore, G.M.3
  • 50
    • 0029202363 scopus 로고
    • The impact of direct refinement against 13C alpha and 13C beta chemical shifts on protein structure determination by NMR
    • Kuszewski J., Qin J., Gronenborn A.M., Clore G.M. The impact of direct refinement against 13C alpha and 13C beta chemical shifts on protein structure determination by NMR. J. Magn. Res. B. 106:1995;92-96.
    • (1995) J. Magn. Res. B , vol.106 , pp. 92-96
    • Kuszewski, J.1    Qin, J.2    Gronenborn, A.M.3    Clore, G.M.4
  • 51
    • 0030000912 scopus 로고    scopus 로고
    • Improving the quality of NMR and crystallographic structures by means of a conformational potential derived from structure databases
    • Kuszewski J., Gronenborn A.M., Clore G.M. Improving the quality of NMR and crystallographic structures by means of a conformational potential derived from structure databases. Prot. Sci. 5:1996;1067-1080.
    • (1996) Prot. Sci. , vol.5 , pp. 1067-1080
    • Kuszewski, J.1    Gronenborn, A.M.2    Clore, G.M.3
  • 53
    • 0000127585 scopus 로고
    • Automated refinement of protein models
    • Lamzin V.S., Wilson K.S. Automated refinement of protein models. Acta Cryst. D. 49:1993;129-147.
    • (1993) Acta Cryst. D , vol.49 , pp. 129-147
    • Lamzin, V.S.1    Wilson, K.S.2
  • 54
    • 0023430366 scopus 로고
    • Monte Carlo-minimization approach to the multiple-minima problem in protein folding
    • Li Z., Scheraga H.A. Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc. Natl. Acad. Sci. USA. 84:1987;6611-6615.
    • (1987) Proc. Natl. Acad. Sci. USA , vol.84 , pp. 6611-6615
    • Li, Z.1    Scheraga, H.A.2
  • 55
    • 0028063256 scopus 로고
    • Protein simulations using techniques suitable for very large systems: The cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics
    • Mathiowetz A.M., Jain A., Karasawa N., Goddard W.A. Protein simulations using techniques suitable for very large systems: the cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics. Proteins Structure Function Genetics. 20:1994;227-247.
    • (1994) Proteins Structure Function Genetics , vol.20 , pp. 227-247
    • Mathiowetz, A.M.1    Jain, A.2    Karasawa, N.3    Goddard, W.A.4
  • 57
    • 0028379642 scopus 로고
    • Coupling constants again: Experimental restraints in structure refinement
    • Mierke D.F., Huber T., Kessler H.J. Coupling constants again: experimental restraints in structure refinement. Comput. Aided Mol. Des. 8:1994;29-40.
    • (1994) Comput. Aided Mol. Des. , vol.8 , pp. 29-40
    • Mierke, D.F.1    Huber, T.2    Kessler, H.J.3
  • 58
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov G.N., Vagin A.A., Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Cryst. D. 53:1997;240-255.
    • (1997) Acta Cryst. D , vol.53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 59
    • 0027446891 scopus 로고
    • X-ray analyses of aspartic proteinases. V. Structure and refinement at 2.0 Å resolution of the aspartic proteinase from Mucor pusillus
    • Newman M., Watson F., Roychowdhury P., Jones H., Badasso M., Cleasby A., Wood S.P., Tickle I.J., Blundell T.L. X-ray analyses of aspartic proteinases. V. Structure and refinement at 2.0 Å resolution of the aspartic proteinase from Mucor pusillus. J. Mol. Biol. 230:1993;260-283.
    • (1993) J. Mol. Biol. , vol.230 , pp. 260-283
    • Newman, M.1    Watson, F.2    Roychowdhury, P.3    Jones, H.4    Badasso, M.5    Cleasby, A.6    Wood, S.P.7    Tickle, I.J.8    Blundell, T.L.9
  • 60
    • 0028907436 scopus 로고
    • Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulfide connectivities
    • Nilges M. Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulfide connectivities. J. Mol. Biol. 245:1995;645-660.
    • (1995) J. Mol. Biol. , vol.245 , pp. 645-660
    • Nilges, M.1
  • 61
    • 0030271733 scopus 로고    scopus 로고
    • Structure calculation from NMR data
    • Nilges M. Structure calculation from NMR data. Curr. Opin. Struct. Biol. 6:1996;617-623.
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 617-623
    • Nilges, M.1
  • 62
    • 0023732144 scopus 로고
    • Determination of three dimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms
    • Nilges M., Clore G.M., Gronenborn A.M. Determination of three dimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms. FEBS Lett. 239:1988;129-136.
    • (1988) FEBS Lett. , vol.239 , pp. 129-136
    • Nilges, M.1    Clore, G.M.2    Gronenborn, A.M.3
  • 63
    • 0024285896 scopus 로고
    • Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations
    • Nilges M., Clore G.M., Gronenborn A.M. Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations. FEBS Lett. 229:1988;317-324.
    • (1988) FEBS Lett. , vol.229 , pp. 317-324
    • Nilges, M.1    Clore, G.M.2    Gronenborn, A.M.3
  • 64
    • 0023998438 scopus 로고
    • Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints: Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2
    • Nilges M., Gronenborn A.M., Brunger A.T., Clore G.M. Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints: application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Protein Eng. 2:1988;27-38.
    • (1988) Protein Eng. , vol.2 , pp. 27-38
    • Nilges, M.1    Gronenborn, A.M.2    Brunger, A.T.3    Clore, G.M.4
  • 66
    • 0029283884 scopus 로고
    • Chemical shifts and three-dimensional protein structures.
    • Oldfield E. Chemical shifts and three-dimensional protein structures. J. Biomol. NMR. 5:1995;217-225.
    • (1995) J. Biomol. NMR , vol.5 , pp. 217-225
    • Oldfield, E.1
  • 67
    • 0000649842 scopus 로고    scopus 로고
    • Improved structure refinement through maximum likelihood
    • Pannu N.S., Read R.J. Improved structure refinement through maximum likelihood. Acta Cryst. A. 52:1996;659-668.
    • (1996) Acta Cryst. a , vol.52 , pp. 659-668
    • Pannu, N.S.1    Read, R.J.2
  • 68
    • 0032212015 scopus 로고    scopus 로고
    • Incorporation of prior phase information strengthens maximum likelihood structural refinement
    • Pannu N.S., Murshudov G.N., Dodson E.J., Read R.J. Incorporation of prior phase information strengthens maximum likelihood structural refinement. Acta Cryst. D. 54:1998;1285-1294.
    • (1998) Acta Cryst. D , vol.54 , pp. 1285-1294
    • Pannu, N.S.1    Murshudov, G.N.2    Dodson, E.J.3    Read, R.J.4
  • 70
    • 0025186647 scopus 로고
    • Atomic charges for DNA constituents derived from single-crystal X-ray diffraction data
    • Pearlman D.A., Kim S.-H. Atomic charges for DNA constituents derived from single-crystal X-ray diffraction data. J. Mol. Biol. 211:1990;171-187.
    • (1990) J. Mol. Biol. , vol.211 , pp. 171-187
    • Pearlman, D.A.1    Kim, S.-H.2
  • 71
    • 0030809260 scopus 로고    scopus 로고
    • WARP: Improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models
    • Perrakis A., Sixma T.K., Wilson K.S., Lamzin V.S. wARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models. Acta Cryst. D. 53:1997;448-455.
    • (1997) Acta Cryst. D , vol.53 , pp. 448-455
    • Perrakis, A.1    Sixma, T.K.2    Wilson, K.S.3    Lamzin, V.S.4
  • 73
    • 84944812409 scopus 로고
    • Improved Fourier coefficients for maps using phases from partial structures with errors
    • Read R.J. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Cryst. A. 42:1986;140-149.
    • (1986) Acta Cryst. a , vol.42 , pp. 140-149
    • Read, R.J.1
  • 74
    • 0000771669 scopus 로고
    • Structure-factor probabilities for related structures
    • Read R.J. Structure-factor probabilities for related structures. Acta Cryst. A. 46:1990;900-912.
    • (1990) Acta Cryst. a , vol.46 , pp. 900-912
    • Read, R.J.1
  • 75
    • 0028070557 scopus 로고
    • Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic structure refinement
    • Rice L.M., Brunger A.T. Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Proteins Structure Function Genetics. 19:1994;277-290.
    • (1994) Proteins Structure Function Genetics , vol.19 , pp. 277-290
    • Rice, L.M.1    Brunger, A.T.2
  • 76
    • 0001645813 scopus 로고    scopus 로고
    • Phase improvement by multi-start simulated annealing refinement and structure factor averaging
    • Rice L.M., Shamoo Y., Brunger A.T. Phase improvement by multi-start simulated annealing refinement and structure factor averaging. J. Appl. Cryst. 31:1998;798-805.
    • (1998) J. Appl. Cryst. , vol.31 , pp. 798-805
    • Rice, L.M.1    Shamoo, Y.2    Brunger, A.T.3
  • 77
    • 0002660809 scopus 로고
    • The detection of sub-units within the crystallographic asymmetric unit
    • Rossmann M.G., Blow D.M. The detection of sub-units within the crystallographic asymmetric unit. Acta Cryst. A. 15:1962;24-51.
    • (1962) Acta Cryst. a , vol.15 , pp. 24-51
    • Rossmann, M.G.1    Blow, D.M.2
  • 78
    • 11744387198 scopus 로고
    • Stochastic exploration of molecular mechanics energy surfaces: Hunting for the global minimum
    • Saunders M. Stochastic exploration of molecular mechanics energy surfaces: hunting for the global minimum. J. Am. Chem. Soc. 109:1987;3150-3152.
    • (1987) J. Am. Chem. Soc. , vol.109 , pp. 3150-3152
    • Saunders, M.1
  • 79
    • 0030059610 scopus 로고    scopus 로고
    • Ribonuclease from Streptomyces aureofaciens at atomic resolution
    • Sevcik J., Dauter Z., Lamzin V.S., Wilson K.S. Ribonuclease from Streptomyces aureofaciens at atomic resolution. Acta Cryst. D. 52:1996;327-344.
    • (1996) Acta Cryst. D , vol.52 , pp. 327-344
    • Sevcik, J.1    Dauter, Z.2    Lamzin, V.S.3    Wilson, K.S.4
  • 80
    • 0031047632 scopus 로고    scopus 로고
    • Crystal structure of the two RNA-binding domains of human hnRNP A1 at 1.75 Å resolution
    • Shamoo Y., Krueger U., Rice L.M., Williams K.R., Steitz T.A. Crystal structure of the two RNA-binding domains of human hnRNP A1 at 1.75 Å resolution. Nat. Struct. Biol. 3:1997;215-222.
    • (1997) Nat. Struct. Biol. , vol.3 , pp. 215-222
    • Shamoo, Y.1    Krueger, U.2    Rice, L.M.3    Williams, K.R.4    Steitz, T.A.5
  • 81
    • 84977296485 scopus 로고
    • The refinement of southern bean mosaic virus in reciprocal space
    • Silva A.M., Rossmann M.G. The refinement of southern bean mosaic virus in reciprocal space. Acta Cryst. B. 41:1985;147-157.
    • (1985) Acta Cryst. B , vol.41 , pp. 147-157
    • Silva, A.M.1    Rossmann, M.G.2
  • 82
    • 0028887396 scopus 로고
    • Full-matrix refinement of the protein crambin at 0.83 Å and 130 K
    • Stec B., Zhou R., Teeter M.M. Full-matrix refinement of the protein crambin at 0.83 Å and 130 K. Acta Cryst. D. 51:1995;663-681.
    • (1995) Acta Cryst. D , vol.51 , pp. 663-681
    • Stec, B.1    Zhou, R.2    Teeter, M.M.3
  • 83
    • 0030621858 scopus 로고    scopus 로고
    • Torsion angle molecular dynamics is a new, efficient tool for NMR structure calculation
    • Stein E.G., Rice L.M., Brunger A.T. Torsion angle molecular dynamics is a new, efficient tool for NMR structure calculation. J. Magn. Reson. B. 124:1997;154-164.
    • (1997) J. Magn. Reson. B , vol.124 , pp. 154-164
    • Stein, E.G.1    Rice, L.M.2    Brunger, A.T.3
  • 84
    • 0001549117 scopus 로고
    • Structure-factor least-squares refinement procedure for macromolecular structure using constrained and restrained parameters
    • Sussman J.L., Holbrook S.R., Church G.M., Kim S.-H. Structure-factor least-squares refinement procedure for macromolecular structure using constrained and restrained parameters. Acta Cryst. A. 33:1977;800-804.
    • (1977) Acta Cryst. a , vol.33 , pp. 800-804
    • Sussman, J.L.1    Holbrook, S.R.2    Church, G.M.3    Kim, S.-H.4
  • 85
    • 0027661179 scopus 로고
    • Metropolis Monte Carlo calculations of DNA structure using internal coordinates and NMR distance restraints: An alternative method for generating a high-resolution solution structure
    • Ulyanov N.B., Schmitz U., James T.L. Metropolis Monte Carlo calculations of DNA structure using internal coordinates and NMR distance restraints: an alternative method for generating a high-resolution solution structure. J. Biomol. NMR. 3:1993;547-568.
    • (1993) J. Biomol. NMR , vol.3 , pp. 547-568
    • Ulyanov, N.B.1    Schmitz, U.2    James, T.L.3
  • 86
    • 22944467757 scopus 로고
    • Computer experiments on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules
    • Verlet L. Computer experiments on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 159:1967;98-105.
    • (1967) Phys. Rev. , vol.159 , pp. 98-105
    • Verlet, L.1
  • 87
    • 0032213133 scopus 로고    scopus 로고
    • Structural parameters for proteins derived from the atomic resolution (1.09 Å) structure of a designed variant of the colE1 ROP protein
    • Vlassi M., Dauter Z., Wilson K.S., Kokkinidis M. Structural parameters for proteins derived from the atomic resolution (1.09 Å) structure of a designed variant of the colE1 ROP protein. Acta Cryst. D. 54:1998;1245-1260.
    • (1998) Acta Cryst. D , vol.54 , pp. 1245-1260
    • Vlassi, M.1    Dauter, Z.2    Wilson, K.S.3    Kokkinidis, M.4
  • 88
    • 0025304137 scopus 로고
    • Refinement of the influenza virus haemagglutinin by simulated annealing
    • Weis W.I., Brunger A.T., Skehel J.J., Wiley D.C. Refinement of the influenza virus haemagglutinin by simulated annealing. J. Mol. Biol. 212:1989;737-761.
    • (1989) J. Mol. Biol. , vol.212 , pp. 737-761
    • Weis, W.I.1    Brunger, A.T.2    Skehel, J.J.3    Wiley, D.C.4
  • 90
    • 0029353627 scopus 로고
    • Structure determination from NOESY intensities using a metropolis simulated-annealing (MSA) refinement of dihedral angles
    • Xu Y., Krishna N.R. Structure determination from NOESY intensities using a metropolis simulated-annealing (MSA) refinement of dihedral angles. J. Mag. Res. B. 108:1995;192-196.
    • (1995) J. Mag. Res. B , vol.108 , pp. 192-196
    • Xu, Y.1    Krishna, N.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.