메뉴 건너뛰기




Volumn 268, Issue 1, 1997, Pages 209-225

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

Author keywords

Computer simulation; Knowledge based scoring functions; Multiple sequence alignment; Protein folding; Structure prediction

Indexed keywords

PROTEIN;

EID: 0031585984     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.0959     Document Type: Article
Times cited : (1158)

References (54)
  • 1
    • 0028883794 scopus 로고
    • Determination of the conformation of folding initiation sites in proteins by computer simulation
    • Avbelj F., Moult J. Determination of the conformation of folding initiation sites in proteins by computer simulation. Proteins: Struct. Funct. Genet. 23:1995;129-141.
    • (1995) Proteins: Struct. Funct. Genet. , vol.23 , pp. 129-141
    • Avbelj, F.1    Moult, J.2
  • 2
    • 0028351287 scopus 로고
    • An improved pair potential to recognize native protein folds
    • Bauer A., Beyer A. An improved pair potential to recognize native protein folds. Proteins: Struct. Funct. Genet. 18:1994;254-261.
    • (1994) Proteins: Struct. Funct. Genet. , vol.18 , pp. 254-261
    • Bauer, A.1    Beyer, A.2
  • 4
    • 0028328263 scopus 로고
    • An evolutionary approach to folding small a-helical proteins that uses sequence information and an empirical guiding fitness function
    • Bowie J. U., Eisenberg D. An evolutionary approach to folding small a-helical proteins that uses sequence information and an empirical guiding fitness function. Proc. Natl Acad. Sci. USA. 91:1994;4436-4440.
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 4436-4440
    • Bowie, J.U.1    Eisenberg, D.2
  • 5
    • 0025341237 scopus 로고
    • Identification of protein folds: Matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures
    • Bowie J. U., Clarke N. D., Pabo C. O., Sauer R. T. Identification of protein folds: matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures. Proteins: Struct. Funct. Genet. 7:1990;257-264.
    • (1990) Proteins: Struct. Funct. Genet. , vol.7 , pp. 257-264
    • Bowie, J.U.1    Clarke, N.D.2    Pabo, C.O.3    Sauer, R.T.4
  • 6
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie J. U., Luthy R., Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 253:1991;164-170.
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Luthy, R.2    Eisenberg, D.3
  • 8
    • 0019001660 scopus 로고
    • On the prediction of protein structure: The significance of the root-mean-square deviation
    • Cohen F. E., Sternberg M. J. On the prediction of protein structure: The significance of the root-mean-square deviation. J. Mol. Biol. 138:1980;321-333.
    • (1980) J. Mol. Biol. , vol.138 , pp. 321-333
    • Cohen, F.E.1    Sternberg, M.J.2
  • 9
    • 0029980527 scopus 로고    scopus 로고
    • Identifying the tertiary fold of small proteins with different topologies from sequence and secondary structure using the genetic algorithm and extended criteria specific for strand regions
    • Dandekar T., Argos P. Identifying the tertiary fold of small proteins with different topologies from sequence and secondary structure using the genetic algorithm and extended criteria specific for strand regions. J. Mol. Biol. 256:1996;645-660.
    • (1996) J. Mol. Biol. , vol.256 , pp. 645-660
    • Dandekar, T.1    Argos, P.2
  • 10
    • 0030595366 scopus 로고    scopus 로고
    • Multiple sequence information for threading algorithms
    • Defay T., Cohen F. Multiple sequence information for threading algorithms. J. Mol. Biol. 262:1996;314-323.
    • (1996) J. Mol. Biol. , vol.262 , pp. 314-323
    • Defay, T.1    Cohen, F.2
  • 11
    • 0019522383 scopus 로고
    • Crystallographic refinement and atomic models of a human FC fragment and its complex with fragment B of protein A from staphylococcus areus at 2.9 and 2.8 angstroms resolution
    • Deisenhofer J. Crystallographic refinement and atomic models of a human FC fragment and its complex with fragment B of protein A from staphylococcus areus at 2.9 and 2.8 angstroms resolution. Biochemistry. 20:1981;2361-2370.
    • (1981) Biochemistry , vol.20 , pp. 2361-2370
    • Deisenhofer, J.1
  • 14
    • 79952608525 scopus 로고
    • Accurate bond and angle parameters for X-ray protein structure refinement
    • Engh R., Huber R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta. Crystallog. sect. A. 47:1991;392-400.
    • (1991) Acta. Crystallog. Sect. a , vol.47 , pp. 392-400
    • Engh, R.1    Huber, R.2
  • 15
    • 0028066936 scopus 로고
    • Comparison of systematic search and database methods for constructing segments of protein structure
    • Fidelis K., Stern P. S., Bacon D., Moult J. Comparison of systematic search and database methods for constructing segments of protein structure. Protein Eng. 7:1994;953-960.
    • (1994) Protein Eng. , vol.7 , pp. 953-960
    • Fidelis, K.1    Stern, P.S.2    Bacon, D.3    Moult, J.4
  • 17
    • 0025769350 scopus 로고
    • A novel, highly stable fold of the immunoglobin binding domain of streptococcal protein G
    • Gronenborn A. M., Clore G. M. A novel, highly stable fold of the immunoglobin binding domain of streptococcal protein G. Science. 253:1991;657-661.
    • (1991) Science , vol.253 , pp. 657-661
    • Gronenborn, A.M.1    Clore, G.M.2
  • 18
    • 0029112501 scopus 로고
    • Recurring local sequence motifs in proteins
    • Han K., Baker D. Recurring local sequence motifs in proteins. J. Mol. Biol. 251:1995;176-187.
    • (1995) J. Mol. Biol. , vol.251 , pp. 176-187
    • Han, K.1    Baker, D.2
  • 19
    • 0029898244 scopus 로고    scopus 로고
    • Global properties of the mapping between local sequence and local structure in proteins
    • Han K., Baker D. Global properties of the mapping between local sequence and local structure in proteins. Proc. Natl Acad. Sci. USA. 93:1996;5814-5818.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 5814-5818
    • Han, K.1    Baker, D.2
  • 20
    • 0029977162 scopus 로고    scopus 로고
    • Using substitution probabilities to improve position-specific scoring matrices
    • Henikoff J. G., Henikoff S. Using substitution probabilities to improve position-specific scoring matrices. CABIOS. 12:1996;135-143.
    • (1996) CABIOS , vol.12 , pp. 135-143
    • Henikoff, J.G.1    Henikoff, S.2
  • 21
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff S., Henikoff J. G. Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA. 89:1992;10915-10919.
    • (1992) Proc. Natl Acad. Sci. USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 22
    • 0027092678 scopus 로고
    • Selection of a representative set of structures from the Brookhaven Protein Data Bank
    • Hobohm U., Scharf M., Schneider R., Sander C. Selection of a representative set of structures from the Brookhaven Protein Data Bank. Protein Sci. 1:1992;409-417.
    • (1992) Protein Sci. , vol.1 , pp. 409-417
    • Hobohm, U.1    Scharf, M.2    Schneider, R.3    Sander, C.4
  • 23
    • 0029101826 scopus 로고
    • Recognizing native folds by the arrangement of hydrophobic and polar residues
    • Huang E. S., Subbiah S., Levitt M. Recognizing native folds by the arrangement of hydrophobic and polar residues. J. Mol. Biol. 252:1995;709-720.
    • (1995) J. Mol. Biol. , vol.252 , pp. 709-720
    • Huang, E.S.1    Subbiah, S.2    Levitt, M.3
  • 24
    • 0029942661 scopus 로고    scopus 로고
    • Structure-derived potentials and protein simulations
    • Jernigan R. L., Bahar I. Structure-derived potentials and protein simulations. Curr. Opin. Struct. Biol. 6:1996;195-209.
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 195-209
    • Jernigan, R.L.1    Bahar, I.2
  • 25
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones D. T., Taylor W. R., Thornton J. M. A new approach to protein fold recognition. Nature. 358:1992;86-89.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 26
    • 0025188837 scopus 로고
    • Crystal structure of an engrailed homeodomain/DNA complex at 2.8 angstroms resolution: A framework for understanding homeodomain/DNA interactions
    • Kissinger C. R., Liu B., Martin-Blanco E., Kornberg T. B., Pabo C. O. Crystal structure of an engrailed homeodomain/DNA complex at 2.8 angstroms resolution: a framework for understanding homeodomain/DNA interactions. Cell. 63:1990;579-590.
    • (1990) Cell , vol.63 , pp. 579-590
    • Kissinger, C.R.1    Liu, B.2    Martin-Blanco, E.3    Kornberg, T.B.4    Pabo, C.O.5
  • 27
    • 0028318094 scopus 로고
    • Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches
    • Kocher J. P., Rooman M. J., Wodak S. J. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J. Mol. Biol. 235:1994;1598-1613.
    • (1994) J. Mol. Biol. , vol.235 , pp. 1598-1613
    • Kocher, J.P.1    Rooman, M.J.2    Wodak, S.J.3
  • 28
    • 0028326042 scopus 로고
    • Monte Carlo simulations of protein folding. II. Application to Protein A, ROP, and Crambin
    • Kolinski A., Skolnick J. Monte Carlo simulations of protein folding. II. Application to Protein A, ROP, and Crambin. Proteins: Struct. Funct. Genet. 18:1994;353-366.
    • (1994) Proteins: Struct. Funct. Genet. , vol.18 , pp. 353-366
    • Kolinski, A.1    Skolnick, J.2
  • 29
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
    • (1991) J. Appl. Crystallog. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 30
  • 31
    • 0023644998 scopus 로고
    • Structure of the C-terminal domain of the ribosomal protein L7/L12 from Escherichia coli at 1.7 A
    • Leijonmarck M., Liljas A. Structure of the C-terminal domain of the ribosomal protein L7/L12 from Escherichia coli at 1.7 A. J. Mol. Biol. 195:1987;555-579.
    • (1987) J. Mol. Biol. , vol.195 , pp. 555-579
    • Leijonmarck, M.1    Liljas, A.2
  • 32
    • 0031588693 scopus 로고    scopus 로고
    • Folding kinetics of CheY mutants with enhanced native [alpha]-helix propensities
    • López-Hernández E., Cronet P., Serrano L., Muñoz V. Folding kinetics of CheY mutants with enhanced native [alpha]-helix propensities. J. Mol. Biol. 266:1997;610-620.
    • (1997) J. Mol. Biol. , vol.266 , pp. 610-620
    • López-Hernández, E.1    Cronet, P.2    Serrano, L.3    Muñoz, V.4
  • 33
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
    • Miyazawa S., Jernigan R. L. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol. 256:1996;623-644.
    • (1996) J. Mol. Biol. , vol.256 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 34
    • 0024961628 scopus 로고
    • Structure of the amino-terminal domain of phage 434 repressor at 2.0 angstroms resolution
    • Mondragon A., Subbiah S., Alamo S. C., Drottar M., Harrison S. C. Structure of the amino-terminal domain of phage 434 repressor at 2.0 angstroms resolution. J. Mol. Biol. 205:1989a;189-200.
    • (1989) J. Mol. Biol. , vol.205 , pp. 189-200
    • Mondragon, A.1    Subbiah, S.2    Alamo, S.C.3    Drottar, M.4    Harrison, S.C.5
  • 35
    • 0024961623 scopus 로고
    • Structure of phage 434 cro protein at 2.35 angstroms resolutions
    • Mondragon A., Wolberger C., Harrison S. C. Structure of phage 434 cro protein at 2.35 angstroms resolutions. J. Mol. Biol. 205:1989b;179-188.
    • (1989) J. Mol. Biol. , vol.205 , pp. 179-188
    • Mondragon, A.1    Wolberger, C.2    Harrison, S.C.3
  • 36
    • 0028283339 scopus 로고
    • An algorithm to generate low-resolution protein tertiary structures from knowledge of secondary structure
    • Monge A., Friesner R. A., Honig B. An algorithm to generate low-resolution protein tertiary structures from knowledge of secondary structure. Proc. Natl Acad. Sci. USA. 91:1994;5027-5029.
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 5027-5029
    • Monge, A.1    Friesner, R.A.2    Honig, B.3
  • 37
    • 0028897718 scopus 로고
    • Computer Modeling of Protein Folding: Conformational and energetic analysis of reduced and detailed protein models
    • Monge A., Lathrop E. J. P., Gunn J. R., Shenkin P. S., Friesner R. A. Computer Modeling of Protein Folding: conformational and energetic analysis of reduced and detailed protein models. J. Mol. Biol. 247:1995;995-1012.
    • (1995) J. Mol. Biol. , vol.247 , pp. 995-1012
    • Monge, A.1    Lathrop, E.J.P.2    Gunn, J.R.3    Shenkin, P.S.4    Friesner, R.A.5
  • 38
    • 0028955505 scopus 로고
    • Predicting the helix packing of globular proteins by self-correcting distance geometry
    • Mumenthaler C., Braun W. Predicting the helix packing of globular proteins by self-correcting distance geometry. Protein Sci. 4:1995;863-871.
    • (1995) Protein Sci. , vol.4 , pp. 863-871
    • Mumenthaler, C.1    Braun, W.2
  • 39
    • 0002682169 scopus 로고    scopus 로고
    • Local versus nonlocal interactions in protein folding and stability - an experimentalist's point of view
    • Munoz V., Serrano L. Local versus nonlocal interactions in protein folding and stability - an experimentalist's point of view. Folding Design. 1:1996;R71-R77.
    • (1996) Folding Design , vol.1
    • Munoz, V.1    Serrano, L.2
  • 40
    • 0029987862 scopus 로고    scopus 로고
    • Energy functions that discriminate X-ray and near-native folds from well-constructed decoys
    • Park B., Levitt M. Energy functions that discriminate X-ray and near-native folds from well-constructed decoys. J. Mol. Biol. 258:1996;367-392.
    • (1996) J. Mol. Biol. , vol.258 , pp. 367-392
    • Park, B.1    Levitt, M.2
  • 41
    • 0031557390 scopus 로고    scopus 로고
    • Factors affecting the ability of energy functions to discriminate correct from incorrect folds
    • Park B. H., Huang E. S., Levitt M. Factors affecting the ability of energy functions to discriminate correct from incorrect folds. J. Mol. Biol. 1997.
    • (1997) J. Mol. Biol.
    • Park, B.H.1    Huang, E.S.2    Levitt, M.3
  • 42
    • 0029984690 scopus 로고    scopus 로고
    • Genetic algorithms for protein structure prediction
    • Pederson J. T., Moult J. Genetic algorithms for protein structure prediction. Curr. Opin. Struct. Biol. 6:1996;227-231.
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 227-231
    • Pederson, J.T.1    Moult, J.2
  • 43
    • 0031052147 scopus 로고    scopus 로고
    • A desolvation barrier to the hydrophobic cluster formation may contribution to the rate limiting step in protein folding
    • Rank J., Baker D. A desolvation barrier to the hydrophobic cluster formation may contribution to the rate limiting step in protein folding. Protein Sci. 6:1997;347-354.
    • (1997) Protein Sci. , vol.6 , pp. 347-354
    • Rank, J.1    Baker, D.2
  • 44
    • 0028158628 scopus 로고
    • PhD - an automatic mail server for protein secondary structure prediction
    • Rost B., Sander C., Schneider R. PhD - an automatic mail server for protein secondary structure prediction. Comput. Appl. Biosci. 10:1994;53-60.
    • (1994) Comput. Appl. Biosci. , vol.10 , pp. 53-60
    • Rost, B.1    Sander, C.2    Schneider, R.3
  • 45
    • 0026030641 scopus 로고
    • Database of homology-derived protein structures and the structural meaning of sequence alignment
    • Sander C., Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins: Struct. Funct. Genet. 9:1991;56-68.
    • (1991) Proteins: Struct. Funct. Genet. , vol.9 , pp. 56-68
    • Sander, C.1    Schneider, R.2
  • 46
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force
    • Sippl M. J. Calculation of conformational ensembles from potentials of mean force. J. Mol. Biol. 213:1990;859-883.
    • (1990) J. Mol. Biol. , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 47
    • 0027650879 scopus 로고
    • Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures
    • Sippl M. J. Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. J. Comp. Aided Mol. Design. 7:1993;473-501.
    • (1993) J. Comp. Aided Mol. Design , vol.7 , pp. 473-501
    • Sippl, M.J.1
  • 48
    • 0029055313 scopus 로고
    • LINUS: A hierarchic procedure to predict the fold of a protein
    • Srinivasan R., Rose G. D. LINUS: A hierarchic procedure to predict the fold of a protein. Proteins: Struct. Funct. Genet. 22:1995;81-99.
    • (1995) Proteins: Struct. Funct. Genet. , vol.22 , pp. 81-99
    • Srinivasan, R.1    Rose, G.D.2
  • 49
    • 0028841399 scopus 로고
    • A simple protein folding algorithm using a binary code and secondary structure constraints
    • Sun S., Thomas P. T., Dill K. A. A simple protein folding algorithm using a binary code and secondary structure constraints. Protein Eng. 8:1995;769-778.
    • (1995) Protein Eng. , vol.8 , pp. 769-778
    • Sun, S.1    Thomas, P.T.2    Dill, K.A.3
  • 50
    • 0026503169 scopus 로고
    • Proline cis-trans isomers in calbindin D9K observed by X-ray crystallography
    • Svensson L. A., Thulin E., Forsen S. Proline cis-trans isomers in calbindin D9K observed by X-ray crystallography. J. Mol. Biol. 223:1992;601-606.
    • (1992) J. Mol. Biol. , vol.223 , pp. 601-606
    • Svensson, L.A.1    Thulin, E.2    Forsen, S.3
  • 51
    • 0029976427 scopus 로고    scopus 로고
    • Statistical potentials extracted from protein structures: How accurate are they?
    • Thomas P. D., Dill K. A. Statistical potentials extracted from protein structures: how accurate are they? J. Mol. Biol. 257:1996;457-469.
    • (1996) J. Mol. Biol. , vol.257 , pp. 457-469
    • Thomas, P.D.1    Dill, K.A.2
  • 52
    • 0024435638 scopus 로고
    • A computer program to dynamically simulate protein folding: Studies with crambin
    • Wilson C., Doniach S. A computer program to dynamically simulate protein folding: studies with crambin. Proteins: Struct. Funct. Genet. 6:1989;193-209.
    • (1989) Proteins: Struct. Funct. Genet. , vol.6 , pp. 193-209
    • Wilson, C.1    Doniach, S.2
  • 53
    • 0027199670 scopus 로고
    • Protein secondary structure prediction using nearest-neighbor methods
    • Yi T. M., Lander E. S. Protein secondary structure prediction using nearest-neighbor methods. J. Mol. Biol. 232:1993;1117-1129.
    • (1993) J. Mol. Biol. , vol.232 , pp. 1117-1129
    • Yi, T.M.1    Lander, E.S.2
  • 54
    • 0030048675 scopus 로고    scopus 로고
    • Folding proteins with a simple energy function and extensive conformational searching
    • Yue K., Dill K. A. Folding proteins with a simple energy function and extensive conformational searching. Protein Sci. 5:1996;254-261.
    • (1996) Protein Sci. , vol.5 , pp. 254-261
    • Yue, K.1    Dill, K.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.