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Volumn 61, Issue 3, 2006, Pages 966-988

Advances in protein structure prediction and de novo protein design: A review

Author keywords

De novo protein design; Force field development; Loop structure prediction; Protein folding

Indexed keywords

DATABASE SYSTEMS; POLYPEPTIDES; PROBLEM SOLVING;

EID: 27844505722     PISSN: 00092509     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ces.2005.04.009     Document Type: Article
Times cited : (202)

References (234)
  • 3
    • 0032552252 scopus 로고    scopus 로고
    • A global optimization method for general twice-differentiable NLPs - II. Implementation and computational results
    • C.S. Adjiman, I.P. Androulakis, and C.A. Floudas A global optimization method for general twice-differentiable NLPs - II. Implementation and computational results Computers and Chemical Engineering 22 1998 1159 1179
    • (1998) Computers and Chemical Engineering , vol.22 , pp. 1159-1179
    • Adjiman, C.S.1    Androulakis, I.P.2    Floudas, C.A.3
  • 4
    • 0032552250 scopus 로고    scopus 로고
    • A global optimization method for general twice-differentiable NLPs - I. Theoretical advances
    • C.S. Adjiman, S. Dallwig, C.A. Floudas, and A. Neumaier A global optimization method for general twice-differentiable NLPs - I. Theoretical advances Computers and Chemical Engineering 22 1998 1137 1158
    • (1998) Computers and Chemical Engineering , vol.22 , pp. 1137-1158
    • Adjiman, C.S.1    Dallwig, S.2    Floudas, C.A.3    Neumaier, A.4
  • 9
    • 0036681387 scopus 로고    scopus 로고
    • A novel fold recognition method using composite predicted secondary structures
    • Y. An, and R.A. Friesner A novel fold recognition method using composite predicted secondary structures Proteins: Structure, Function, and Bioinformatics 48 2002 352 366
    • (2002) Proteins: Structure, Function, and Bioinformatics , vol.48 , pp. 352-366
    • An, Y.1    Friesner, R.A.2
  • 10
  • 11
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • C.B. Anfinsen Principles that govern the folding of protein chains Science 181 4096 1973 223 230
    • (1973) Science , vol.181 , Issue.4096 , pp. 223-230
    • Anfinsen, C.B.1
  • 12
    • 0031566950 scopus 로고    scopus 로고
    • Inter-residue potential in globular proteins and the dominance of highly specific hydrophillic interactions at close separation
    • I. Bahar, and R.L. Jernigan Inter-residue potential in globular proteins and the dominance of highly specific hydrophillic interactions at close separation Journal of Molecular Biology 266 1997 195 214
    • (1997) Journal of Molecular Biology , vol.266 , pp. 195-214
    • Bahar, I.1    Jernigan, R.L.2
  • 18
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • J.U. Bowie, R. Lüthy, and D. Eisenberg A method to identify protein sequences that fold into a known three-dimensional structure Science 253 5016 1991 164 170
    • (1991) Science , vol.253 , Issue.5016 , pp. 164-170
    • Bowie, J.U.1    Lüthy, R.2    Eisenberg, D.3
  • 20
    • 0026016378 scopus 로고
    • The frequency of ion-pair substructures in proteins is quantitaively related to electrostatic potential. A statistical model for nonbonded interactions
    • S.H. Bryant, and C.E. Lawrence The frequency of ion-pair substructures in proteins is quantitaively related to electrostatic potential. A statistical model for nonbonded interactions Proteins: Structure, Function, and Bioinformatics 9 1991 108 119
    • (1991) Proteins: Structure, Function, and Bioinformatics , vol.9 , pp. 108-119
    • Bryant, S.H.1    Lawrence, C.E.2
  • 21
    • 0034081255 scopus 로고    scopus 로고
    • Mechanical unfolding of a beta-hairpin using molecular dynamics
    • Z. Bryant, V.S. Pande, and D.S. Rokhsar Mechanical unfolding of a beta-hairpin using molecular dynamics Biophysical Journal 78 2000 584 589
    • (2000) Biophysical Journal , vol.78 , pp. 584-589
    • Bryant, Z.1    Pande, V.S.2    Rokhsar, D.S.3
  • 22
    • 0031746429 scopus 로고    scopus 로고
    • From coiled coils to small globular proteins: Design of a native-like three-helix bundle
    • J.W. Bryson, J.R. Desjarlais, T.M. Handel, and W.F. DeGrado From coiled coils to small globular proteins: design of a native-like three-helix bundle Protein Science 7 1998 1404 1414
    • (1998) Protein Science , vol.7 , pp. 1404-1414
    • Bryson, J.W.1    Desjarlais, J.R.2    Handel, T.M.3    Degrado, W.F.4
  • 23
    • 0027122748 scopus 로고
    • One thousand families for the molecular biologist
    • C. Chothia One thousand families for the molecular biologist Nature 357 1992 543 544
    • (1992) Nature , vol.357 , pp. 543-544
    • Chothia, C.1
  • 26
    • 0035002440 scopus 로고    scopus 로고
    • Constructing smooth potential functions for protein folding
    • G.M. Crippen Constructing smooth potential functions for protein folding Journal of Molecular Graphics and Modelling 19 2001 87 93
    • (2001) Journal of Molecular Graphics and Modelling , vol.19 , pp. 87-93
    • Crippen, G.M.1
  • 28
    • 0346492912 scopus 로고    scopus 로고
    • Improved conformational space annealing method to treat beta-structure with the UNRES force-field and to enhance scalability of parallel implementation
    • C. Czaplewski, A. Liwo, J. Pillardy, S. Oldziej, and H.A. Scheraga Improved conformational space annealing method to treat beta-structure with the UNRES force-field and to enhance scalability of parallel implementation Polymer 45 2004 677 686
    • (2004) Polymer , vol.45 , pp. 677-686
    • Czaplewski, C.1    Liwo, A.2    Pillardy, J.3    Oldziej, S.4    Scheraga, H.A.5
  • 29
    • 0842334823 scopus 로고    scopus 로고
    • Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds
    • C. Czaplewski, S. Oldziej, A. Liwo, and H.A. Scheraga Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds Protein Engineering Design and Selection 17 2004 29 36
    • (2004) Protein Engineering Design and Selection , vol.17 , pp. 29-36
    • Czaplewski, C.1    Oldziej, S.2    Liwo, A.3    Scheraga, H.A.4
  • 31
    • 0030793767 scopus 로고    scopus 로고
    • De novo protein design: Fully automated sequence selection
    • B.I. Dahiyat, and S.L. Mayo De novo protein design: fully automated sequence selection Science 278 1997 82 87
    • (1997) Science , vol.278 , pp. 82-87
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 32
    • 0041387567 scopus 로고    scopus 로고
    • A large scale test of computational protein design: Folding and stability of nine completely redesigned globular proteins
    • G. Dantas, B. Kuhlman, D. Callender, M. Wong, and D. Baker A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins Journal of Molecular Biology 332 2003 449 460
    • (2003) Journal of Molecular Biology , vol.332 , pp. 449-460
    • Dantas, G.1    Kuhlman, B.2    Callender, D.3    Wong, M.4    Baker, D.5
  • 33
    • 0037375615 scopus 로고    scopus 로고
    • Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the generalized Born solvation model
    • P.I.W. de Bakker, M.A. DePristo, D.F. Burke, and T.L. Blundell Ab initio construction of polypeptide fragments: accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the generalized Born solvation model Proteins: Structure, Function, and Bioinformatics 51 2003 21 40
    • (2003) Proteins: Structure, Function, and Bioinformatics , vol.51 , pp. 21-40
    • De Bakker, P.I.W.1    Depristo, M.A.2    Burke, D.F.3    Blundell, T.L.4
  • 34
    • 0035107308 scopus 로고    scopus 로고
    • CODA: A combined algorithm for predicting the structurally variable regions of protein models
    • C.M. Deane, and T.L. Blundell CODA: a combined algorithm for predicting the structurally variable regions of protein models Protein Science 10 2001 599 612
    • (2001) Protein Science , vol.10 , pp. 599-612
    • Deane, C.M.1    Blundell, T.L.2
  • 36
    • 0028858499 scopus 로고
    • De novo design of the hydrophobic cores of proteins
    • J.R. Desjarlais, and T.M. Handel De novo design of the hydrophobic cores of proteins Protein Science 4 1995 2006 2018
    • (1995) Protein Science , vol.4 , pp. 2006-2018
    • Desjarlais, J.R.1    Handel, T.M.2
  • 37
    • 0033516509 scopus 로고    scopus 로고
    • Side-chain and backbone flexibiity in protein core design
    • J.R. Desjarlais, and T.M. Handel Side-chain and backbone flexibiity in protein core design Journal of Molecular Biology 290 1999 305 318
    • (1999) Journal of Molecular Biology , vol.290 , pp. 305-318
    • Desjarlais, J.R.1    Handel, T.M.2
  • 38
    • 0026589733 scopus 로고
    • The dead-end elimination theorem and its use in protein side-chain positioning
    • J. Desmet, M. Maeyer, B. Hazes, and I. Lasters The dead-end elimination theorem and its use in protein side-chain positioning Nature 356 1992 539 542
    • (1992) Nature , vol.356 , pp. 539-542
    • Desmet, J.1    Maeyer, M.2    Hazes, B.3    Lasters, I.4
  • 39
    • 0025370815 scopus 로고
    • Dominant forces in protein folding
    • K.A. Dill Dominant forces in protein folding Biochemistry 29 1990 7133 7155
    • (1990) Biochemistry , vol.29 , pp. 7133-7155
    • Dill, K.A.1
  • 41
    • 0019774747 scopus 로고
    • Molecular engineering: An approach to the development of general capabilities for molecular manipulation
    • K.E. Drexler Molecular engineering: an approach to the development of general capabilities for molecular manipulation Proceedings of the National Academy of Sciences of the United States of America 78 9 1981 5275 5278
    • (1981) Proceedings of the National Academy of Sciences of the United States of America , vol.78 , Issue.9 , pp. 5275-5278
    • Drexler, K.E.1
  • 43
    • 3042655537 scopus 로고    scopus 로고
    • Computational design of a biologically active enzyme
    • M.A. Dwyer, L.L. Looger, and H.W. Hellinga Computational design of a biologically active enzyme Science 304 2004 1967 1971
    • (2004) Science , vol.304 , pp. 1967-1971
    • Dwyer, M.A.1    Looger, L.L.2    Hellinga, H.W.3
  • 44
    • 0031075977 scopus 로고    scopus 로고
    • Solvation free energies of peptides: Comparison of approximate continuum solvation models with accurate solution of the Poisson-Boltzmann equation
    • S. Edinger, C. Cortis, P. Shenkin, and R. Friesner Solvation free energies of peptides: comparison of approximate continuum solvation models with accurate solution of the Poisson-Boltzmann equation Journal of Physical Chemistry B 101 1997 1190 1197
    • (1997) Journal of Physical Chemistry B , vol.101 , pp. 1190-1197
    • Edinger, S.1    Cortis, C.2    Shenkin, P.3    Friesner, R.4
  • 47
    • 0037436405 scopus 로고    scopus 로고
    • Flexibility of α-helices: Results of a statistical analysis of database protein structures
    • E.G. Emberly, R. Mukhopadhyay, C. Tang, and N.S. Wingreen Flexibility of α -helices: results of a statistical analysis of database protein structures Journal of Molecular Biology 327 2003 229 237
    • (2003) Journal of Molecular Biology , vol.327 , pp. 229-237
    • Emberly, E.G.1    Mukhopadhyay, R.2    Tang, C.3    Wingreen, N.S.4
  • 50
    • 0032588985 scopus 로고    scopus 로고
    • Prediction of protein tertiary structure to low resolution: Performance for a large and structurally diverse test set
    • V.A. Eyrich, D.M. Standley, and R.A. Friesner Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set Journal of Molecular Biology 288 1999 725 742
    • (1999) Journal of Molecular Biology , vol.288 , pp. 725-742
    • Eyrich, V.A.1    Standley, D.M.2    Friesner, R.A.3
  • 51
    • 0031694147 scopus 로고    scopus 로고
    • The de novo design of a rubredoxin-like Fe site
    • E. Farinas, and L. Regan The de novo design of a rubredoxin-like Fe site Protein Science 7 1998 1939 1946
    • (1998) Protein Science , vol.7 , pp. 1939-1946
    • Farinas, E.1    Regan, L.2
  • 53
    • 0033810049 scopus 로고    scopus 로고
    • Modeling of loops in protein structures
    • A. Fiser, R.K.G. Do, and A. Sali Modeling of loops in protein structures Protein Science 9 2000 1753 1773
    • (2000) Protein Science , vol.9 , pp. 1753-1773
    • Fiser, A.1    Do, R.K.G.2    Sali, A.3
  • 58
    • 0041919601 scopus 로고    scopus 로고
    • Discrimination of native loop conformations in membrane proteins: Decoy library design and evaluation of effective energy scoring functions
    • L.R. Forrest, and T.B. Woolf Discrimination of native loop conformations in membrane proteins: decoy library design and evaluation of effective energy scoring functions Proteins: Structure, Function, and Bioinformatics 52 2003 491 509
    • (2003) Proteins: Structure, Function, and Bioinformatics , vol.52 , pp. 491-509
    • Forrest, L.R.1    Woolf, T.B.2
  • 60
    • 0032516785 scopus 로고    scopus 로고
    • From synthetic coiled coils to functional proteins: Automated design of a receptor for the calmodulin-binding domain of calcineurin
    • G. Ghirlanda, J.D. Lear, A. Lombardi, and W.F. DeGrado From synthetic coiled coils to functional proteins: automated design of a receptor for the calmodulin-binding domain of calcineurin Journal of Molecular Biology 281 1998 379 391
    • (1998) Journal of Molecular Biology , vol.281 , pp. 379-391
    • Ghirlanda, G.1    Lear, J.D.2    Lombardi, A.3    Degrado, W.F.4
  • 61
    • 0041530316 scopus 로고    scopus 로고
    • NMR and temperature-jump measurements of de novo designed proteins demonstrate rapid folding in the absence of explicit selection for kinetics
    • B. Gillespie, D.M. Vu, P.S. Shah, S.A. Marshall, R.B. Dyer, S.L. Mayo, and K.W. Plaxco NMR and temperature-jump measurements of de novo designed proteins demonstrate rapid folding in the absence of explicit selection for kinetics Journal of Molecular Biology 330 2003 813 819
    • (2003) Journal of Molecular Biology , vol.330 , pp. 813-819
    • Gillespie, B.1    Vu, D.M.2    Shah, P.S.3    Marshall, S.A.4    Dyer, R.B.5    Mayo, S.L.6    Plaxco, K.W.7
  • 63
    • 0028212927 scopus 로고
    • Efficient rotamer elimination applied to protein side-chains and related spin glasses
    • R.F. Goldstein Efficient rotamer elimination applied to protein side-chains and related spin glasses Biophysical Journal 66 1994 1335 1340
    • (1994) Biophysical Journal , vol.66 , pp. 1335-1340
    • Goldstein, R.F.1
  • 66
    • 0031576336 scopus 로고    scopus 로고
    • Torsion angle dynamics for NMR structure calculation with the new program DYANA
    • P. Güntert, C. Mumenthaler, and K. Wüthrich Torsion angle dynamics for NMR structure calculation with the new program DYANA Journal of Molecular Biology 273 1997 283 298
    • (1997) Journal of Molecular Biology , vol.273 , pp. 283-298
    • Güntert, P.1    Mumenthaler, C.2    Wüthrich, K.3
  • 67
  • 68
    • 0032553587 scopus 로고    scopus 로고
    • High-resolution protein design with backbone freedom
    • P.B. Harbury, J.J. Plecs, B. Tidor, T. Alber, and P.S. Kim High-resolution protein design with backbone freedom Science 282 1998 1462 1467
    • (1998) Science , vol.282 , pp. 1462-1467
    • Harbury, P.B.1    Plecs, J.J.2    Tidor, B.3    Alber, T.4    Kim, P.S.5
  • 69
    • 0001138328 scopus 로고
    • Algorithm AS 136: A K-means clustering algorithm
    • J.A. Hartigan, and M.A. Wong Algorithm AS 136: a K-means clustering algorithm Applied Statistics 28 1979 100 108
    • (1979) Applied Statistics , vol.28 , pp. 100-108
    • Hartigan, J.A.1    Wong, M.A.2
  • 70
    • 3042577367 scopus 로고    scopus 로고
    • De novo proteins from designed combinatorial libraries
    • M.H. Hecht, A. Das, A. Go, L.H. Bradley, and Y. Wei De novo proteins from designed combinatorial libraries Protein Science 13 2004 1711 1723
    • (2004) Protein Science , vol.13 , pp. 1711-1723
    • Hecht, M.H.1    Das, A.2    Go, A.3    Bradley, L.H.4    Wei, Y.5
  • 73
    • 33751385054 scopus 로고
    • Macroscopic models of aqueous solutions - Biological and chemical applications
    • B. Honig, K. Sharp, and A. Yang Macroscopic models of aqueous solutions - biological and chemical applications Journal of Physical Chemistry 97 1993 1101 1109
    • (1993) Journal of Physical Chemistry , vol.97 , pp. 1101-1109
    • Honig, B.1    Sharp, K.2    Yang, A.3
  • 76
    • 0031298075 scopus 로고    scopus 로고
    • Successful ab initio prediction of the tertiary structure of NK-lysin using multiple sequences and recognized supersecondary structural motifs
    • D.T. Jones Successful ab initio prediction of the tertiary structure of NK-lysin using multiple sequences and recognized supersecondary structural motifs Proteins: Structure Function and Bioinformatics S1 1997 185 191
    • (1997) Proteins: Structure Function and Bioinformatics , vol.1 , pp. 185-191
    • Jones, D.T.1
  • 77
    • 0033537993 scopus 로고    scopus 로고
    • GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
    • D.T. Jones GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences Journal of Molecular Biology 287 1999 797 815
    • (1999) Journal of Molecular Biology , vol.287 , pp. 797-815
    • Jones, D.T.1
  • 78
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position specific scoring matrices
    • D.T. Jones Protein secondary structure prediction based on position specific scoring matrices Journal of Molecular Biology 292 1999 195 202
    • (1999) Journal of Molecular Biology , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 81
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • D.T. Jones, W.R. Taylor, and J.M. Thornton 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
  • 82
    • 0031008576 scopus 로고    scopus 로고
    • Hydrophobicity regained
    • P.A. Karplus Hydrophobicity regained Protein Science 6 1997 1302 1307
    • (1997) Protein Science , vol.6 , pp. 1302-1307
    • Karplus, P.A.1
  • 83
    • 0032438987 scopus 로고    scopus 로고
    • Hidden Markov models for detecting remote protein homologies
    • K. Karplus, C. Barret, and R. Hughey Hidden Markov models for detecting remote protein homologies Bioinformatics 14 10 1998 846 856
    • (1998) Bioinformatics , vol.14 , Issue.10 , pp. 846-856
    • Karplus, K.1    Barret, C.2    Hughey, R.3
  • 86
    • 0034595501 scopus 로고    scopus 로고
    • Enhanced genome annotation using structural profiles in the program 3D-PSSM
    • L.A. Kelley, R.M. MacCallum, and M.J.E. Sternberg Enhanced genome annotation using structural profiles in the program 3D-PSSM Journal of Molecular Biology 299 2 2000 499 520
    • (2000) Journal of Molecular Biology , vol.299 , Issue.2 , pp. 499-520
    • Kelley, L.A.1    MacCallum, R.M.2    Sternberg, M.J.E.3
  • 87
    • 0242720595 scopus 로고    scopus 로고
    • The PDB is a covering set of small protein structures
    • D. Kihara, and J. Skolnick The PDB is a covering set of small protein structures Journal of Molecular Biology 334 2003 793 802
    • (2003) Journal of Molecular Biology , vol.334 , pp. 793-802
    • Kihara, D.1    Skolnick, J.2
  • 88
    • 0142184275 scopus 로고    scopus 로고
    • PROSPECT II: Protein structure prediction program for genome-scale applications
    • D. Kim, D. Xu, J. Guo, K. Ellrott, and Y. Xu PROSPECT II: protein structure prediction program for genome-scale applications Protein Engineering 16 9 2003 641 650
    • (2003) Protein Engineering , vol.16 , Issue.9 , pp. 641-650
    • Kim, D.1    Xu, D.2    Guo, J.3    Ellrott, K.4    Xu, Y.5
  • 90
    • 0037472756 scopus 로고    scopus 로고
    • Prediction of beta-sheet topology and disulfide bridges in polypeptides
    • J.L. Klepeis, and C.A. Floudas Prediction of beta-sheet topology and disulfide bridges in polypeptides Journal of Computational Chemistry 24 2003 191 208
    • (2003) Journal of Computational Chemistry , vol.24 , pp. 191-208
    • Klepeis, J.L.1    Floudas, C.A.2
  • 91
  • 92
    • 0141642142 scopus 로고    scopus 로고
    • ASTRO-FOLD: A combinatorial and global optimization framework for ab initio prediction of three-dimensional structures of proteins from the amino acid sequence
    • J.L. Klepeis, and C.A. Floudas ASTRO-FOLD: a combinatorial and global optimization framework for ab initio prediction of three-dimensional structures of proteins from the amino acid sequence Biophysical Journal 85 2003 2119 2146
    • (2003) Biophysical Journal , vol.85 , pp. 2119-2146
    • Klepeis, J.L.1    Floudas, C.A.2
  • 93
    • 15744373547 scopus 로고    scopus 로고
    • Analysis and prediction of loop segments in protein structure
    • Klepeis, J.L., Floudas, C.A., 2005. Analysis and prediction of loop segments in protein structure. Computers and Chemical Engineering 29, 423-436.
    • (2005) Computers and Chemical Engineering , vol.29 , pp. 423-436
    • Klepeis, J.L.1    Floudas, C.A.2
  • 94
    • 0037445044 scopus 로고    scopus 로고
    • A new class of hybrid global optimization algorithms for peptide structure prediction. Integrated hybrids
    • J.L. Klepeis, M.T. Pieja, and C.A. Floudas A new class of hybrid global optimization algorithms for peptide structure prediction. Integrated hybrids Computer Physics Communication 151 2003 121 140
    • (2003) Computer Physics Communication , vol.151 , pp. 121-140
    • Klepeis, J.L.1    Pieja, M.T.2    Floudas, C.A.3
  • 95
    • 0037305932 scopus 로고    scopus 로고
    • Hybrid global optimization algorithms for protein structure prediction: Alternating hybrids
    • J.L. Klepeis, M.T. Pieja, and C.A. Floudas Hybrid global optimization algorithms for protein structure prediction: alternating hybrids Biophysical Journal 84 2003 869 882
    • (2003) Biophysical Journal , vol.84 , pp. 869-882
    • Klepeis, J.L.1    Pieja, M.T.2    Floudas, C.A.3
  • 98
    • 12944263648 scopus 로고    scopus 로고
    • Ab initio prediction of the three-dimensional structure of a de novo designed protein: A double blind case study
    • J.L. Klepeis, Y.N. Wei, M.H. Hecht, and C.A. Floudas Ab initio prediction of the three-dimensional structure of a de novo designed protein: a double blind case study Proteins: Structure, Function, and Bioinformatics 58 2005 560 570
    • (2005) Proteins: Structure, Function, and Bioinformatics , vol.58 , pp. 560-570
    • Klepeis, J.L.1    Wei, Y.N.2    Hecht, M.H.3    Floudas, C.A.4
  • 99
    • 0033550206 scopus 로고    scopus 로고
    • De novo protein design. I. In search of stability and specificity
    • P. Koehl, and M. Levitt De novo protein design. I. In search of stability and specificity Journal of Molecular Biology 293 1999 1161 1181
    • (1999) Journal of Molecular Biology , vol.293 , pp. 1161-1181
    • Koehl, P.1    Levitt, M.2
  • 100
    • 0033550264 scopus 로고    scopus 로고
    • De novo protein design. II. Plasticity in sequence space
    • P. Koehl, and M. Levitt De novo protein design. II. Plasticity in sequence space Journal of Molecular Biology 293 1999 1183 1193
    • (1999) Journal of Molecular Biology , vol.293 , pp. 1183-1193
    • Koehl, P.1    Levitt, M.2
  • 101
    • 0035936702 scopus 로고    scopus 로고
    • Statistical theory for protein combinatorial libraries, packing interactions, backbone flexibility, and the sequence variability of a main-chain structure
    • H. Kono, and J.G. Saven Statistical theory for protein combinatorial libraries, packing interactions, backbone flexibility, and the sequence variability of a main-chain structure Journal of Molecular Biology 306 2001 607 628
    • (2001) Journal of Molecular Biology , vol.306 , pp. 607-628
    • Kono, H.1    Saven, J.G.2
  • 102
    • 3142758686 scopus 로고    scopus 로고
    • Automated protein structure homology modeling: A progress report
    • J. Kopp, and T. Schwede Automated protein structure homology modeling: a progress report Pharmacogenomics Journal 5 4 2004 405 416
    • (2004) Pharmacogenomics Journal , vol.5 , Issue.4 , pp. 405-416
    • Kopp, J.1    Schwede, T.2
  • 103
    • 0037470581 scopus 로고    scopus 로고
    • An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
    • T. Kortemme, A.V. Morozov, and D. Baker An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes Journal of Molecular Biology 326 2003 1239 1259
    • (2003) Journal of Molecular Biology , vol.326 , pp. 1239-1259
    • Kortemme, T.1    Morozov, A.V.2    Baker, D.3
  • 107
    • 1342324030 scopus 로고    scopus 로고
    • Exploring folding free energy landscapes using computational protein design
    • B. Kuhlman, and D. Baker Exploring folding free energy landscapes using computational protein design Current Opinion in Structural Biology 14 2004 89 95
    • (2004) Current Opinion in Structural Biology , vol.14 , pp. 89-95
    • Kuhlman, B.1    Baker, D.2
  • 108
    • 0036300662 scopus 로고    scopus 로고
    • Accurate computer-based design of a new backbone conformation in the second turn of protein l
    • B. Kuhlman, J.W. O'Neill, D.E. Kim, K.Y.J. Zhang, and D. Baker Accurate computer-based design of a new backbone conformation in the second turn of protein l Journal of Molecular Biology 315 2002 471 477
    • (2002) Journal of Molecular Biology , vol.315 , pp. 471-477
    • Kuhlman, B.1    O'Neill, J.W.2    Kim, D.E.3    Zhang, K.Y.J.4    Baker, D.5
  • 110
    • 0036892389 scopus 로고    scopus 로고
    • Thoroughly sampling sequence space: Large-scale protein design of structural ensembles
    • S.M. Larson, J.L. England, J.R. Desjarlais, and V.S. Pande Thoroughly sampling sequence space: large-scale protein design of structural ensembles Protein Science 11 2002 2804 2813
    • (2002) Protein Science , vol.11 , pp. 2804-2813
    • Larson, S.M.1    England, J.L.2    Desjarlais, J.R.3    Pande, V.S.4
  • 111
    • 0028015988 scopus 로고
    • The protein threading problem with sequence amino-acid interaction preferences is NP-complete
    • R.H. Lathrop The protein threading problem with sequence amino-acid interaction preferences is NP-complete Protein Engineering 7 9 1994 1059 1068
    • (1994) Protein Engineering , vol.7 , Issue.9 , pp. 1059-1068
    • Lathrop, R.H.1
  • 112
    • 0028223845 scopus 로고
    • Predicting protein mutant energetics by self-consistent ensemble optimization
    • C. Lee Predicting protein mutant energetics by self-consistent ensemble optimization Journal of Molecular Biology 236 1994 918 939
    • (1994) Journal of Molecular Biology , vol.236 , pp. 918-939
    • Lee, C.1
  • 113
    • 0000542451 scopus 로고    scopus 로고
    • Conformational space annealing by parallel computations: Extensive conformational search of met-enkephalin and the 20-residue membrane-bound portion of melittin
    • J. Lee, and H.A. Scheraga Conformational space annealing by parallel computations: extensive conformational search of met-enkephalin and the 20-residue membrane-bound portion of melittin International Journal of Quantum Chemistry 75 1999 255 265
    • (1999) International Journal of Quantum Chemistry , vol.75 , pp. 255-265
    • Lee, J.1    Scheraga, H.A.2
  • 114
    • 0001176785 scopus 로고    scopus 로고
    • New optimization method for conformational energy calculations on polypeptides: Conformational space annealing
    • J. Lee, H.A. Scheraga, and S. Rackovsky New optimization method for conformational energy calculations on polypeptides: conformational space annealing Journal of Computational Chemistry 18 1997 1222 1232
    • (1997) Journal of Computational Chemistry , vol.18 , pp. 1222-1232
    • Lee, J.1    Scheraga, H.A.2    Rackovsky, S.3
  • 115
    • 0032146482 scopus 로고    scopus 로고
    • Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing
    • J. Lee, H.A. Scheraga, and S. Rackovsky Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing Biopolymers 46 1998 103 115
    • (1998) Biopolymers , vol.46 , pp. 103-115
    • Lee, J.1    Scheraga, H.A.2    Rackovsky, S.3
  • 118
    • 4043058565 scopus 로고    scopus 로고
    • Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing
    • J. Lee, S.-Y. Kim, K. Joo, I. Kim, and J. Lee Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing Proteins: Structure Function and Bioinformatics 56 2004 704 714
    • (2004) Proteins: Structure Function and Bioinformatics , vol.56 , pp. 704-714
    • Lee, J.1    Kim, S.-Y.2    Joo, K.3    Kim, I.4    Lee, J.5
  • 120
    • 0001861319 scopus 로고
    • How to fold graciously
    • P. Debrunner J.C.M. Tsibris E.M. Münck University of Illinois Press Urbana
    • C. Levinthal How to fold graciously P. Debrunner J.C.M. Tsibris E.M. Münck Mossbauer Spectroscopy in Biological Systems 1969 University of Illinois Press Urbana 22 24
    • (1969) Mossbauer Spectroscopy in Biological Systems , pp. 22-24
    • Levinthal, C.1
  • 122
    • 0037110580 scopus 로고    scopus 로고
    • Designability of protein structures: A lattice-model study using the Miyazawa-Jernigan matrix
    • H. Li, C. Tang, and N.S. Wingreen Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix Proteins: Structure, Function, and Bioinformatics 49 2002 403 412
    • (2002) Proteins: Structure, Function, and Bioinformatics , vol.49 , pp. 403-412
    • Li, H.1    Tang, C.2    Wingreen, N.S.3
  • 125
    • 0036322695 scopus 로고    scopus 로고
    • Target space for structural genomics revisited
    • J. Liu, and B. Rost Target space for structural genomics revisited Bioinformatics 18 7 2002 922 933
    • (2002) Bioinformatics , vol.18 , Issue.7 , pp. 922-933
    • Liu, J.1    Rost, B.2
  • 127
    • 0000095892 scopus 로고    scopus 로고
    • A united-residue force field for off-lattice protein structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data
    • A. Liwo, S. Oldziej, M.R. Pincus, R.J. Wawak, S. Rackovsky, and H.A. Scheraga A united-residue force field for off-lattice protein structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data Journal of Computational Chemistry 18 1997 849 873
    • (1997) Journal of Computational Chemistry , vol.18 , pp. 849-873
    • Liwo, A.1    Oldziej, S.2    Pincus, M.R.3    Wawak, R.J.4    Rackovsky, S.5    Scheraga, H.A.6
  • 128
    • 0000095890 scopus 로고    scopus 로고
    • A united-residue force field for off-lattice protein structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by z-score optimization
    • A. Liwo, M.R. Pincus, R.J. Wawak, S. Rackovsky, S. Oldziej, and H.A. Scheraga A united-residue force field for off-lattice protein structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by z -score optimization Journal of Computational Chemistry 18 1997 874 887
    • (1997) Journal of Computational Chemistry , vol.18 , pp. 874-887
    • Liwo, A.1    Pincus, M.R.2    Wawak, R.J.3    Rackovsky, S.4    Oldziej, S.5    Scheraga, H.A.6
  • 129
    • 0031309121 scopus 로고    scopus 로고
    • Design of a knowledge-based force field for off-lattice simulations of protein structure
    • A. Liwo, S. Odziej, R. Kamierkiewicz, M. Groth, and C. Czaplewski Design of a knowledge-based force field for off-lattice simulations of protein structure Acta Biochimica Polonica 44 1997 527 547
    • (1997) Acta Biochimica Polonica , vol.44 , pp. 527-547
    • Liwo, A.1    Odziej, S.2    Kamierkiewicz, R.3    Groth, M.4    Czaplewski, C.5
  • 131
    • 0035424584 scopus 로고    scopus 로고
    • Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field
    • A. Liwo, C. Czaplewski, J. Pillardy, and H.A. Scheraga Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field Journal of Chemical Physics 115 2001 2323 2347
    • (2001) Journal of Chemical Physics , vol.115 , pp. 2323-2347
    • Liwo, A.1    Czaplewski, C.2    Pillardy, J.3    Scheraga, H.A.4
  • 133
    • 3142681595 scopus 로고    scopus 로고
    • Parametrization of backbone-electrostatic and multibody contributions to the UNRES force field for protein-structure prediction from ab initio energy surfaces of model systems
    • A. Liwo, S. Odziej, C. Czaplewski, U. Kozlowska, and H.A. Scheraga Parametrization of backbone-electrostatic and multibody contributions to the UNRES force field for protein-structure prediction from ab initio energy surfaces of model systems Journal of Physical Chemistry B 108 2004 9421 9438
    • (2004) Journal of Physical Chemistry B , vol.108 , pp. 9421-9438
    • Liwo, A.1    Odziej, S.2    Czaplewski, C.3    Kozlowska, U.4    Scheraga, H.A.5
  • 134
    • 0035896029 scopus 로고    scopus 로고
    • Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: Implications for protein design and structural genomics
    • L.L. Looger, and H.W. Hellinga Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics Journal of Molecular Biology 307 2001 429 445
    • (2001) Journal of Molecular Biology , vol.307 , pp. 429-445
    • Looger, L.L.1    Hellinga, H.W.2
  • 135
    • 0038752617 scopus 로고    scopus 로고
    • Computational design of receptor and sensor proteins with novel functions
    • L.L. Looger, M.A. Dwyer, J.J. Smith, and H.W. Hellinga Computational design of receptor and sensor proteins with novel functions Nature 423 2003 185 190
    • (2003) Nature , vol.423 , pp. 185-190
    • Looger, L.L.1    Dwyer, M.A.2    Smith, J.J.3    Hellinga, H.W.4
  • 138
    • 0035882533 scopus 로고    scopus 로고
    • A distance-dependent knowledge-based potential for improved protein structure selection
    • H. Lu, and J. Skolnick A distance-dependent knowledge-based potential for improved protein structure selection Proteins: Structure, Function, and Bioinformatics 44 2001 223 232
    • (2001) Proteins: Structure, Function, and Bioinformatics , vol.44 , pp. 223-232
    • Lu, H.1    Skolnick, J.2
  • 140
    • 0026785519 scopus 로고
    • Contact potential that recognizes the correct folding of globular proteins
    • V.N. Maiorov, and G.M. Crippen Contact potential that recognizes the correct folding of globular proteins Journal of Molecular Biology 227 1992 876 888
    • (1992) Journal of Molecular Biology , vol.227 , pp. 876-888
    • Maiorov, V.N.1    Crippen, G.M.2
  • 141
    • 0031779918 scopus 로고    scopus 로고
    • Design, structure, and stability of a hyperthermophilic protein variant
    • S.M. Malakauskas, and S.L. Mayo Design, structure, and stability of a hyperthermophilic protein variant Nature Structural Biology 5 1998 470 475
    • (1998) Nature Structural Biology , vol.5 , pp. 470-475
    • Malakauskas, S.M.1    Mayo, S.L.2
  • 143
    • 0037079580 scopus 로고    scopus 로고
    • Maximum feasibility guideline in the design and analysis of protein folding potentials
    • J. Meller, M. Wagner, and R. Elber Maximum feasibility guideline in the design and analysis of protein folding potentials Journal of Computational Chemistry 23 2002 111 118
    • (2002) Journal of Computational Chemistry , vol.23 , pp. 111-118
    • Meller, J.1    Wagner, M.2    Elber, R.3
  • 145
    • 0033566614 scopus 로고    scopus 로고
    • An emperical energy potential with a reference state for protein fold and sequence recognition
    • S. Miyazawa, and R.L. Jernigan An emperical energy potential with a reference state for protein fold and sequence recognition Proteins: Structure, Function, and Bioinformatics 36 1999 357 369
    • (1999) Proteins: Structure, Function, and Bioinformatics , vol.36 , pp. 357-369
    • Miyazawa, S.1    Jernigan, R.L.2
  • 146
    • 5944250450 scopus 로고
    • Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids
    • F.A. Momany, R.F. McGuire, A.W. Burgess, and H.A. Scheraga Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids Journal of Physical Chemistry 79 1975 2361 2381
    • (1975) Journal of Physical Chemistry , vol.79 , pp. 2361-2381
    • Momany, F.A.1    McGuire, R.F.2    Burgess, A.W.3    Scheraga, H.A.4
  • 149
    • 0032751746 scopus 로고    scopus 로고
    • Predicting protein three-dimensional structure
    • J. Moult Predicting protein three-dimensional structure Current Opinion in Biotechnology 10 1999 583 588
    • (1999) Current Opinion in Biotechnology , vol.10 , pp. 583-588
    • Moult, J.1
  • 153
    • 0038502170 scopus 로고    scopus 로고
    • Folding dynamics and mechanism of beta-hairpin formation
    • V. Munoz, P.A. Thompson, J. Hofrichter, and W.A. Eaton Folding dynamics and mechanism of beta-hairpin formation Nature 390 1997 196 199
    • (1997) Nature , vol.390 , pp. 196-199
    • Munoz, V.1    Thompson, P.A.2    Hofrichter, J.3    Eaton, W.A.4
  • 155
    • 0028348081 scopus 로고
    • Principles determining the structure of beta-sheet barrels in proteins. I. A theoretical analysis
    • A.G. Murzin, A.M. Lesk, and C. Chothia Principles determining the structure of beta-sheet barrels in proteins. i. a theoretical analysis Journal of Molecular Biology 236 1994 1369 1381
    • (1994) Journal of Molecular Biology , vol.236 , pp. 1369-1381
    • Murzin, A.G.1    Lesk, A.M.2    Chothia, C.3
  • 156
    • 0028330220 scopus 로고
    • Principles determining the structure of beta-sheet barrels in proteins. II. The observed structures
    • A.G. Murzin, A.M. Lesk, and C. Chothia Principles determining the structure of beta-sheet barrels in proteins. ii. the observed structures Journal of Molecular Biology 236 1994 1382 1400
    • (1994) Journal of Molecular Biology , vol.236 , pp. 1382-1400
    • Murzin, A.G.1    Lesk, A.M.2    Chothia, C.3
  • 157
    • 0001731773 scopus 로고
    • Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm with application to proline-containing peptides
    • G. Némethy, K.D. Gibson, K.A. Palmer, C.N. Yoon, G. Paterlini, A. Zagari, S. Rumsey, and H.A. Scheraga Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm with application to proline-containing peptides Journal of Physical Chemistry 96 1992 6472 6484
    • (1992) Journal of Physical Chemistry , vol.96 , pp. 6472-6484
    • Némethy, G.1    Gibson, K.D.2    Palmer, K.A.3    Yoon, C.N.4    Paterlini, G.5    Zagari, A.6    Rumsey, S.7    Scheraga, H.A.8
  • 158
    • 0036208872 scopus 로고    scopus 로고
    • Recent progress in multiple sequence alignment: A survey
    • C. Notredame Recent progress in multiple sequence alignment: a survey Pharmacogenomics Journal 3 1 2002 131 144
    • (2002) Pharmacogenomics Journal , vol.3 , Issue.1 , pp. 131-144
    • Notredame, C.1
  • 160
    • 0033693249 scopus 로고    scopus 로고
    • Potential energy functions for continuous state models of globular proteins
    • Y.Z. Ohkubo, and G.M. Crippen Potential energy functions for continuous state models of globular proteins Journal of Computational Biology 7 2000 363 379
    • (2000) Journal of Computational Biology , vol.7 , pp. 363-379
    • Ohkubo, Y.Z.1    Crippen, G.M.2
  • 161
    • 0028593509 scopus 로고
    • Protein superfamilies and domain superfolds
    • C.A. Orengo, D.T. Jones, and J.M. Thornton Protein superfamilies and domain superfolds Nature 372 1994 631 634
    • (1994) Nature , vol.372 , pp. 631-634
    • Orengo, C.A.1    Jones, D.T.2    Thornton, J.M.3
  • 162
    • 0021108287 scopus 로고
    • Molecular technology. Designing proteins and peptides
    • C. Pabo Molecular technology. Designing proteins and peptides Nature 301 5897 1983 200
    • (1983) Nature , vol.301 , Issue.5897 , pp. 200
    • Pabo, C.1
  • 168
    • 0035782661 scopus 로고    scopus 로고
    • Review: Protein design - Where we were, where we are, where we're going
    • N. Pokala, and T.M. Handel Review: protein design - where we were, where we are, where we're going Journal of Structural Biology 134 2001 269 281
    • (2001) Journal of Structural Biology , vol.134 , pp. 269-281
    • Pokala, N.1    Handel, T.M.2
  • 169
    • 84988112508 scopus 로고
    • An efficient Newton-like method for molecular mechanics energy minimization of large molecules
    • J.W. Ponder, and F.M. Richards An efficient Newton-like method for molecular mechanics energy minimization of large molecules Journal of Computational Chemistry 8 1987 1016 1024
    • (1987) Journal of Computational Chemistry , vol.8 , pp. 1016-1024
    • Ponder, J.W.1    Richards, F.M.2
  • 170
    • 0023155210 scopus 로고
    • Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes
    • J.W. Ponder, and F.M. Richards Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes Journal of Molecular Biology 193 1987 775 791
    • (1987) Journal of Molecular Biology , vol.193 , pp. 775-791
    • Ponder, J.W.1    Richards, F.M.2
  • 172
    • 33845280446 scopus 로고
    • Comparing the polarities of amino acids: Side chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution
    • A. Radzicka, and R. Wolfenden Comparing the polarities of amino acids: side chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution Biochemical Journal 27 1988 1664 1670
    • (1988) Biochemical Journal , vol.27 , pp. 1664-1670
    • Radzicka, A.1    Wolfenden, R.2
  • 173
    • 0026335211 scopus 로고
    • Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with pre-defined geometry
    • F.M. Richards, and H.W. Hellinga Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with pre-defined geometry Journal of Molecular Biology 222 1991 763 785
    • (1991) Journal of Molecular Biology , vol.222 , pp. 763-785
    • Richards, F.M.1    Hellinga, H.W.2
  • 175
    • 0026321752 scopus 로고
    • Construction of new ligand binding sites in proteins of known structure. II. Grafting of a buried transition metal binding site into Escherichia coli thioredoxin
    • F.M. Richards, J.P. Caradonna, and H.W. Hellinga Construction of new ligand binding sites in proteins of known structure. II. Grafting of a buried transition metal binding site into Escherichia coli thioredoxin Journal of Molecular Biology 222 1991 787 803
    • (1991) Journal of Molecular Biology , vol.222 , pp. 787-803
    • Richards, F.M.1    Caradonna, J.P.2    Hellinga, H.W.3
  • 176
    • 0032146488 scopus 로고    scopus 로고
    • New developments of the electrostatically driven Monte Carlo method: Tests on the membrane-bound portion of melittin
    • D. Ripoll, A. Liwo, and H.A. Scheraga New developments of the electrostatically driven Monte Carlo method: tests on the membrane-bound portion of melittin Biopolymers 46 1998 117 126
    • (1998) Biopolymers , vol.46 , pp. 117-126
    • Ripoll, D.1    Liwo, A.2    Scheraga, H.A.3
  • 178
    • 0035109198 scopus 로고    scopus 로고
    • Designed protein G core variants fold to native-like structures: Sequence selection by ORBIT tolerates variation in backbone specification
    • S.A. Ross, C.A. Sarisky, A. Su, and S.L. Mayo Designed protein G core variants fold to native-like structures: sequence selection by ORBIT tolerates variation in backbone specification Protein Science 10 2001 450 454
    • (2001) Protein Science , vol.10 , pp. 450-454
    • Ross, S.A.1    Sarisky, C.A.2    Su, A.3    Mayo, S.L.4
  • 179
    • 0035782925 scopus 로고    scopus 로고
    • Review: Protein secondary structure prediction continues to rise
    • B. Rost Review: protein secondary structure prediction continues to rise Journal of Structural Biology 134 2001 204 218
    • (2001) Journal of Structural Biology , vol.134 , pp. 204-218
    • Rost, B.1
  • 180
    • 0032488962 scopus 로고    scopus 로고
    • An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
    • R. Samudrala, and J. Moult An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction Journal of Molecular Biology 275 1998 895 916
    • (1998) Journal of Molecular Biology , vol.275 , pp. 895-916
    • Samudrala, R.1    Moult, J.2
  • 181
    • 0035471136 scopus 로고    scopus 로고
    • Designing protein energy landscapes
    • J.G. Saven Designing protein energy landscapes Chemical Reviews 101 2001 3113 3130
    • (2001) Chemical Reviews , vol.101 , pp. 3113-3130
    • Saven, J.G.1
  • 183
    • 0038637819 scopus 로고    scopus 로고
    • Connecting statistical and optimized potentials in protein folding via a generalized foldability criterion
    • J.G. Saven Connecting statistical and optimized potentials in protein folding via a generalized foldability criterion Journal of Chemical Physics 118 2003 6133 6136
    • (2003) Journal of Chemical Physics , vol.118 , pp. 6133-6136
    • Saven, J.G.1
  • 186
    • 0031745665 scopus 로고    scopus 로고
    • Protein design: A perspective from simple tractable models
    • E.I. Shakhnovich Protein design: a perspective from simple tractable models Folding and Design 3 1998 45 58
    • (1998) Folding and Design , vol.3 , pp. 45-58
    • Shakhnovich, E.I.1
  • 188
    • 0035967880 scopus 로고    scopus 로고
    • FUGUE: Sequence-structure homology prediction using environment-specific substitution tables and structure-dependent gap penalties
    • J. Shi, L.B. Tom, and M. Kenji FUGUE: sequence-structure homology prediction using environment-specific substitution tables and structure-dependent gap penalties Journal of Molecular Biology 310 2001 243 257
    • (2001) Journal of Molecular Biology , vol.310 , pp. 243-257
    • Shi, J.1    Tom, L.B.2    Kenji, M.3
  • 190
    • 0035979340 scopus 로고    scopus 로고
    • A designed protein with packing between left-handed and right-handed helices
    • S.K. Sia, and P.S. Kim A designed protein with packing between left-handed and right-handed helices Biochemistry 40 2001 8981 8989
    • (2001) Biochemistry , vol.40 , pp. 8981-8989
    • Sia, S.K.1    Kim, P.S.2
  • 191
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • K.T. Simons, C. Kooperberg, C. Huang, and D. Baker Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions Journal of Molecular Biology 268 1997 209 225
    • (1997) Journal of Molecular Biology , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, C.3    Baker, D.4
  • 193
    • 0030983768 scopus 로고    scopus 로고
    • Derivation and testing of pair potential for protein folding. When is quasichemical approximation correct?
    • J. Skolnick, L. Jaroszewski, A. Kolinski, and A. Godzik Derivation and testing of pair potential for protein folding. When is quasichemical approximation correct? Protein Science 6 1997 676 688
    • (1997) Protein Science , vol.6 , pp. 676-688
    • Skolnick, J.1    Jaroszewski, L.2    Kolinski, A.3    Godzik, A.4
  • 194
    • 0031575423 scopus 로고    scopus 로고
    • MONSSTER: A method for folding globular proteins with a small number of distance constraints
    • J. Skolnick, A. Kolinski, and A.R. Oritz MONSSTER: a method for folding globular proteins with a small number of distance constraints Journal of Molecular Biology 265 1997 217 241
    • (1997) Journal of Molecular Biology , vol.265 , pp. 217-241
    • Skolnick, J.1    Kolinski, A.2    Oritz, A.R.3
  • 202
    • 0030762021 scopus 로고    scopus 로고
    • Coupling backbone flexibility and amino acid sequence selection in protein design
    • A. Su, and S.L. Mayo Coupling backbone flexibility and amino acid sequence selection in protein design Protein Science 6 1997 1701 1707
    • (1997) Protein Science , vol.6 , pp. 1701-1707
    • Su, A.1    Mayo, S.L.2
  • 203
    • 0017021957 scopus 로고
    • Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins
    • S. Tanaka, and H.A. Scheraga Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins Macromolecules 9 1976 945 950
    • (1976) Macromolecules , vol.9 , pp. 945-950
    • Tanaka, S.1    Scheraga, H.A.2
  • 205
    • 0034308163 scopus 로고    scopus 로고
    • Distance-dependent, pair potential for protein folding: Results from linear optimization
    • D. Tobi, and R. Elber Distance-dependent, pair potential for protein folding: results from linear optimization Proteins: Structure, Function, and Bioinformatics 41 2000 40 46
    • (2000) Proteins: Structure, Function, and Bioinformatics , vol.41 , pp. 40-46
    • Tobi, D.1    Elber, R.2
  • 209
    • 0000171351 scopus 로고    scopus 로고
    • Pairwise contact potentials are unsuitable for protein folding
    • M. Vendruscolo, and E. Domany Pairwise contact potentials are unsuitable for protein folding Journal of Chemical Physics 109 1998 11101 11108
    • (1998) Journal of Chemical Physics , vol.109 , pp. 11101-11108
    • Vendruscolo, M.1    Domany, E.2
  • 210
    • 0034141931 scopus 로고    scopus 로고
    • Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?
    • M. Vendruscolo, R. Najmanovich, and E. Domany Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading? Proteins: Structure, Function, and Bioinformatics 38 2000 134 148
    • (2000) Proteins: Structure, Function, and Bioinformatics , vol.38 , pp. 134-148
    • Vendruscolo, M.1    Najmanovich, R.2    Domany, E.3
  • 215
    • 2342536436 scopus 로고    scopus 로고
    • Searching for folded proteins in vitro and in silico
    • A.L. Watters, and D. Baker Searching for folded proteins in vitro and in silico European Journal of Biochemistry 271 2004 1615 1622
    • (2004) European Journal of Biochemistry , vol.271 , pp. 1615-1622
    • Watters, A.L.1    Baker, D.2
  • 216
    • 0034682869 scopus 로고    scopus 로고
    • Automatic protein design with all atom force-fields by exact and heuristic optimization
    • L. Wernisch, S. Hery, and S.J. Wodak Automatic protein design with all atom force-fields by exact and heuristic optimization Journal of Molecular Biology 301 2000 713 736
    • (2000) Journal of Molecular Biology , vol.301 , pp. 713-736
    • Wernisch, L.1    Hery, S.2    Wodak, S.J.3
  • 217
    • 0025744588 scopus 로고
    • Computational method for the design of enzymes with altered substrate specificity
    • C. Wilson, J.E. Mace, and D.A. Agard Computational method for the design of enzymes with altered substrate specificity Journal of Molecular Biology 220 1991 495 506
    • (1991) Journal of Molecular Biology , vol.220 , pp. 495-506
    • Wilson, C.1    MacE, J.E.2    Agard, D.A.3
  • 218
    • 0037963208 scopus 로고    scopus 로고
    • An empirical model for electrostatic interactions in proteins incorporating multiple geometry-dependent dielectric constants
    • M.S. Wisz, and H.W. Hellinga An empirical model for electrostatic interactions in proteins incorporating multiple geometry-dependent dielectric constants Proteins: Structure, Function, and Bioinformatics 51 2003 360 377
    • (2003) Proteins: Structure, Function, and Bioinformatics , vol.51 , pp. 360-377
    • Wisz, M.S.1    Hellinga, H.W.2
  • 219
    • 0034733381 scopus 로고    scopus 로고
    • Ab initio construction of protein tertiary structure using a hierarchical approach
    • Y. Xia, E.S. Huang, M. Levitt, and R. Samudrala Ab initio construction of protein tertiary structure using a hierarchical approach Journal of Molecular Biology 300 2000 171 185
    • (2000) Journal of Molecular Biology , vol.300 , pp. 171-185
    • Xia, Y.1    Huang, E.S.2    Levitt, M.3    Samudrala, R.4
  • 221
    • 0242330716 scopus 로고    scopus 로고
    • Assessment of RAPTOR's linear programming approach in CAFASP3
    • J. Xu, and M. Li Assessment of RAPTOR's linear programming approach in CAFASP3 Proteins: Structure, Function, and Bioinformatics 53 2003 579 584
    • (2003) Proteins: Structure, Function, and Bioinformatics , vol.53 , pp. 579-584
    • Xu, J.1    Li, M.2
  • 224
    • 1642575364 scopus 로고    scopus 로고
    • Accurate and efficient loop selections by the DFIRE - Based all atom statistical potential
    • C. Zhang, S. Liu, and Y. Zhou Accurate and efficient loop selections by the DFIRE - based all atom statistical potential Protein Science 13 2003 391 399
    • (2003) Protein Science , vol.13 , pp. 391-399
    • Zhang, C.1    Liu, S.2    Zhou, Y.3
  • 225
    • 1642534609 scopus 로고    scopus 로고
    • An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state
    • C. Zhang, S. Liu, H. Zhou, and Y. Zhou An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state Protein Science 13 2004 400 411
    • (2004) Protein Science , vol.13 , pp. 400-411
    • Zhang, C.1    Liu, S.2    Zhou, H.3    Zhou, Y.4
  • 226
    • 0031916717 scopus 로고    scopus 로고
    • How do potentials derived from structural database relate to "true" potentials?
    • L. Zhang, and J. Skolnick How do potentials derived from structural database relate to "true" potentials? Protein Science 7 1998 112 122
    • (1998) Protein Science , vol.7 , pp. 112-122
    • Zhang, L.1    Skolnick, J.2
  • 227
    • 16644386061 scopus 로고    scopus 로고
    • Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins
    • Y. Zhang, and J. Skolnick Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins Biophysical Journal 87 2004 2647 2655
    • (2004) Biophysical Journal , vol.87 , pp. 2647-2655
    • Zhang, Y.1    Skolnick, J.2
  • 229
    • 1942519275 scopus 로고    scopus 로고
    • SPICKER: A clustering approach to identify near-native protein folds
    • Y. Zhang, and J. Skolnick SPICKER: a clustering approach to identify near-native protein folds Journal of Computational Chemistry 25 2004 865 871
    • (2004) Journal of Computational Chemistry , vol.25 , pp. 865-871
    • Zhang, Y.1    Skolnick, J.2
  • 230
    • 0041843696 scopus 로고    scopus 로고
    • TOUCHSTONE II: A new approach to ab initio protein structure prediction
    • Y. Zhang, A. Kolinski, and J. Skolnick TOUCHSTONE II: a new approach to ab initio protein structure prediction Biophysical Journal 85 2003 1145 1164
    • (2003) Biophysical Journal , vol.85 , pp. 1145-1164
    • Zhang, Y.1    Kolinski, A.2    Skolnick, J.3
  • 231
    • 0036838311 scopus 로고    scopus 로고
    • Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
    • H. Zhou, and Y. Zhou Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction Protein Science 11 2002 2714 2726
    • (2002) Protein Science , vol.11 , pp. 2714-2726
    • Zhou, H.1    Zhou, Y.2
  • 233
    • 0034635349 scopus 로고    scopus 로고
    • Statistical theory of combinatorial libraries of folding proteins: Energetic discrimination of a target structure
    • J. Zou, and J.G. Saven Statistical theory of combinatorial libraries of folding proteins: energetic discrimination of a target structure Journal of Molecular Biology 296 2000 281 294
    • (2000) Journal of Molecular Biology , vol.296 , pp. 281-294
    • Zou, J.1    Saven, J.G.2


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