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Kono, H., & Saven, J. G. (2001). Statistical theory for protein combinatorial libraries. packing interactions, backbone flexibility, and the sequence variability of a main-chain structure11Edited by J. Thornton. Journal of Molecular Biology, 306(3), 607–628.

Authors 2
  1. Hidetoshi Kono (first)
  2. Jeffery G. Saven (additional)
References 119 Referenced 113
  1. 10.1016/S1359-0278(96)00033-8 / Fold. Des. / Improved design of stable and fast-folding model proteins by Abkevich (1996)
  2. 10.1093/nar/25.17.3389 / Nucl. Acids Res. / Gapped BLAST and PSI-BLAST by Altschul (1997)
  3. 10.1073/pnas.93.11.5590 / Proc. Natl Acad. Sci. USA / Active barnase variants with completely random hydrophobic cores by Axe (1996)
  4. 10.1016/S0959-440X(99)80068-2 / Curr Opin. Struct. Biol. / Engineering and design by Baker (1999)
  5. 10.1126/science.8259514 / Science / The role of backbone flexibility in the accommodation of variants that repack the core of T4 lysozyme by Baldwin (1993)
  6. 10.1016/S0076-6879(96)66006-6 / Methods Enzymol. / Superfamily classification in the PIR-international protein sequence database by Barker (1996)
  7. 10.1016/0959-440X(93)90090-8 / Curr. Opin. Struct. Biol. / De novo protein design by Betz (1993)
  8. 10.1006/jmbi.1997.0926 / J. Mol. Biol. / Prediction of protein side-chain rotamers from a backbone-dependent rotamer library by Bower (1997)
  9. 10.1126/science.1853201 / Science / A method to identify protein sequences that fold into a known three-dimensional structure by Bowie (1991)
  10. 10.1073/pnas.84.21.7524 / Proc. Natl Acad. Sci. USA / Spin glasses and the statistical mechanics of protein folding by Bryngelson (1987)
  11. 10.1126/science.270.5238.935 / Science / Protein design by Bryson (1995)
  12. 10.1002/pro.5560070617 / Protein Sci. / From coiled coils to small globular proteins by Bryson (1998)
  13. {'key': '10.1006/jmbi.2000.4422_BIB13', 'first-page': '126', 'article-title': 'How similar must a template protein be for homology modeling by side-chain packing methods?', 'author': 'Chung', 'year': '1996', 'journal-title': 'Pac. Symp. Biocomputing'} / Pac. Symp. Biocomputing / How similar must a template protein be for homology modeling by side-chain packing methods? by Chung (1996)
  14. 10.1126/science.278.5335.82 / Science / De novo protein design by Dahiyat (1997)
  15. 10.1073/pnas.94.19.10172 / Proc. Natl Acad. Sci. USA / Probing the role of packing specificity in protein design by Dahiyat (1997)
  16. 10.1073/pnas.91.6.2146 / Proc. Natl Acad. Sci. USA / Folded proteins occur frequently in libraries of random amino acid sequences by Davidson (1994)
  17. 10.1002/pro.5560041006 / Protein Sci. / De novo design of the hydrophobic cores of proteins by Desjarlais (1995)
  18. 10.1006/jmbi.1999.2866 / J. Mol. Biol. / Side-chain and backbone flexibility in protein core design by Desjarlais (1999)
  19. 10.1038/356539a0 / Nature / The dead-end elimination theorem and its use in protein side-chain positioning by Desmet (1992)
  20. 10.1103/PhysRevLett.76.323 / Phys. Rev. Letters / New algorithm for protein design by Deutsch (1996)
  21. 10.1002/(SICI)1097-0134(19990401)35:1<34::AID-PROT4>3.0.CO;2-Q / Proteins: Struct. Funct. Genet. / Factors that affect the folding ability of proteins by Dinner (1999)
  22. 10.1006/jmbi.1993.1170 / J. Mol. Biol. / Backbone-dependent rotamer library for proteins application to side-chain prediction by Dunbrack (1993)
  23. 10.1002/pro.5560060807 / Protein Sci. / Bayesian statistical analysis of protein side-chain retainer preferences by Dunbrack (1997)
  24. 10.1038/319199a0 / Nature / Solvation energy in protein folding and binding by Eisenberg (1986)
  25. 10.1002/jcc.540160303 / J. Comput. Chem. / The double cubic lattice method by Eisenhaber (1995)
  26. 10.1021/ja00181a020 / J. Am. Chem. Soc. / Enhanced sampling in molecular dynamics by Elber (1990)
  27. {'key': '10.1006/jmbi.2000.4422_BIB27', 'first-page': '369', 'article-title': 'Hydrophobic parameters π of amino acid side chains from the partitioning of N-acetyl-amino acid amides', 'volume': '18', 'author': 'Fauchere', 'year': '1983', 'journal-title': 'Eur. J. Med. Chem. Chim. Therm.'} / Eur. J. Med. Chem. Chim. Therm. / Hydrophobic parameters π of amino acid side chains from the partitioning of N-acetyl-amino acid amides by Fauchere (1983)
  28. 10.1038/351497a0 / Nature / A search for the most stable folds of protein chains by Finkelstein (1991)
  29. 10.1016/0022-2836(92)90693-E / J. Mol. Biol. / Topology fingerprint approach to the inverse protein folding problem by Godzik (1992)
  30. 10.1073/pnas.89.19.9029 / Proc. Natl Acad. Sci. USA / Protein tertiary structure recognition using optimized Hamiltonians with local interactions by Goldstein (1992)
  31. 10.1016/0076-6879(90)83011-W / Methods Enzymol / Profile analysis by Gribskov (1990)
  32. 10.1110/ps.8.12.2734 / Protein Sci / Robustness of protein folding kinetics to surface hydrophobic substitutions by Gu (1999)
  33. 10.1073/pnas.92.18.8408 / Proc. Natl Acad. Sci. USA / Repacking protein cores with backbone freedom by Harbury (1995)
  34. 10.1126/science.282.5393.1462 / Science / High-resolution protein design with backbone freedom by Harbury (1998)
  35. 10.1073/pnas.91.13.5803 / Proc. Natl Acad. Sci. USA / Optimal sequence selection in proteins of known structure by simulated evolution by Hellinga (1994)
  36. 10.1021/ja9733649 / J. Am. Chem. Soc / Solution structure of α2d, nativelike de novo designed protein by Hill (1998)
  37. 10.1016/S0969-2126(00)00130-1 / Structure / A polar, solvent exposed residue can be essential for native protein structure by Hill (2000)
  38. 10.1006/jmbi.1996.0243 / J. Mol. Biol / From structure to sequence and back again by Hinds (1996)
  39. 10.1002/prot.340140208 / Proteins: Struct. Funct. Genet / Fast and simple Monte Carlo algorithm for side chain optimization in proteins by Holm (1992)
  40. 10.1002/(SICI)1097-0134(19981101)33:2<204::AID-PROT5>3.0.CO;2-I / Proteins: Struct. Funct. Genet / Accuracy of side-chain prediciton upon nearnative protein backbone generated by ab initio folding methods by Huang (1998)
  41. 10.1103/PhysRevE.58.R5249 / Phys. Rev. ser. E / Monte Carlo procedure for protein design by Irbäck (1998)
  42. 10.1016/S0969-2126(99)80044-6 / Structure / Design of sequence with good folding properties in coarse-grained protein models by Irbäck (1999)
  43. 10.1110/ps.9.2.403 / Protein Sci / A new approach to the design of uniquely folded thermally stable proteins by Jiang (2000)
  44. 10.1107/S0907444900002195 / Acta Crystallog. sect. D / Crystallization and preliminary X-ray diffraction studies of mutants of B1 IgG-binding domain of protein L from Peptostreptococcus magnus by Johnsen (2000)
  45. 10.1002/pro.5560030405 / Protein Sci / De novo protein design using pairwise potentials and a genetic algorithm by Jones (1994)
  46. 10.1006/jmbi.1999.3091 / J. Mol. Biol / Protein secondary structure prediction based on position-specific scoring matrices by Jones (1999)
  47. 10.1126/science.8259512 / Science / Protein design by binary patterning of polar and nonpolar amino acids by Kamtekar (1993)
  48. 10.1073/pnas.95.9.4982 / Proc. Natl Acad. Sci. USA / The sequences of small proteins are not extensively optimized for rapid folding by natural selection by Kim (1998)
  49. 10.1063/1.477012 / J. Chem. Phys / Linking rates of folding in lattice models of proteins with underlying thermodynamic characteristics by Klimov (1998)
  50. 10.1006/jmbi.1994.1366 / J. Mol. Biol / Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy by Koehl (1994)
  51. 10.1016/S0959-440X(96)80078-9 / Curr. Opin. Struct. Biol / Mean-field minimization methods for biological macromolecules by Koehl (1996)
  52. 10.1073/pnas.96.22.12524 / Proc. Natl Acad. Sci. USA / Structure-based conformational preferences of amino acids by Koehl (1999)
  53. 10.1006/jmbi.1999.3211 / J. Mol. Biol / De novo protein design. I. In search of stability and specificity by Koehl (1999)
  54. 10.1006/jmbi.1999.3212 / J. Mol. Biol / De novo protein design. II. Plasticity in sequence space by Koehl (1999)
  55. 10.1002/prot.340190308 / Proteins: Struct. Funct. Genet / Energy minimization method using automata network for sequence and side-chain conformation prediction from given backbone geometry by Kono (1994)
  56. 10.1002/(SICI)1096-987X(19961115)17:14<1667::AID-JCC8>3.0.CO;2-J / J. Comput. Chem / A new method for side-chain conformation prediction using a Hopfield network and reproduced rotamers by Kona (1996)
  57. 10.1093/protein/11.1.47 / Protein Eng / Designing the hydrophobic core of Thermos lavus malate dehydrogenase based on side-chain packing by Kono (1998)
  58. 10.1107/S0021889891004399 / J. Appl. Crystallog / MOLSCRIPT by Kraulis (1991)
  59. 10.1007/BF01715807 / Mol. Divers / Libraries of random-sequence polypeptides produced with high yield as carboxy-terminal fusions with ubiquitin by LaBean (1995)
  60. 10.1002/pro.5560060605 / Protein Sci / De novo design of the hydrophobic core of ubiquitin by Lazar (1997)
  61. 10.1006/jmbi.1994.1198 / J. Mol. Biol / Prediction protein mutant energetics by self-consistent ensemble optimization by Lee (1994)
  62. 10.1016/S0022-2836(83)80129-6 / J. Mol. Biol / Protein folding by constrained energy minimization and molecular dynamics by Levitt (1983)
  63. 10.1073/pnas.91.1.423 / Proc. Natl Acad. Sci. USA / The crystal structure of a mutant protein with altered but improved hydrophobic core packing by Lim (1994)
  64. 10.1002/1097-0134(20000815)40:3<389::AID-PROT50>3.0.CO;2-2 / Proteins: Struct. Funct. Genet / The penultimate rotamer library by Lovell (2000)
  65. 10.1016/S1359-0278(97)00006-0 / Fold. Des / All in one by Maeyer (1997)
  66. 10.1038/nsb0698-470 / Nature Struct. Biol / Design, structure and stability of a hyperthermophilic protein variant by Malakauskas (1998)
  67. 10.1038/275673a0 / Nature / Hydrophobic character of amino acid residues in globular proteins by Manavalan (1978)
  68. {'key': '10.1006/jmbi.2000.4422_BIB68', 'series-title': 'Statistical Mechanics', 'author': 'McQuarrie', 'year': '1976'} / Statistical Mechanics by McQuarrie (1976)
  69. 10.1063/1.478168 / J. Chem. Phys / Designability, thermodynamic stability and dynamics in protein folding by Mélin (1999)
  70. 10.1002/(SICI)1097-0282(199908)50:2<111::AID-BIP1>3.0.CO;2-N / Biopolymers / Improvement of side-chain modeling in proteins with the self-consitent mean fiedl theory method based on an analysis of the factors influentcing prediction by Mendes (1999)
  71. 10.1016/S0076-6879(97)77028-9 / Methods Enzymol / Raster3D photorealistic molecular graphics by Merritt (1997)
  72. 10.1016/0022-2836(87)90038-6 / J. Mol. Biol / Interior and sufrace of monomeric proteins by Miller (1987)
  73. 10.1006/jmbi.1996.0704 / J. Mol. Biol / How to derive a protein folding potential? A new approach to an old problem by Mirny (1996)
  74. 10.1021/ma00145a039 / Macromolecules / Estimation of effective interresidue contact energies from protein crystal structures by Miyazawa (1985)
  75. 10.1006/jmbi.1996.0114 / J. Mol. Biol / Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading by Miyazawa (1996)
  76. 10.1016/S1359-0278(96)00054-5 / Fold. Des / Design of proteins with selected thermal properties by Morrissey (1996)
  77. 10.1111/j.1399-3011.1980.tb02931.x / Int. J. Pept. Protein Res / Prediction of the surface-interior diagram of globular proteins by an empirical method by Nishikawa (1980)
  78. 10.1016/S0021-9258(19)77210-X / J. Biol. Chem / The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions by Nozaki (1971)
  79. 10.1063/1.468195 / J. Chem. Phys / Folding thermodynamics and kinetics of imprinted renaturable heteropolymers by Pande (1994)
  80. 10.1073/pnas.91.26.12976 / Proc. Natl Acad. Sci. USA / Thermodynamic procedure to synthesize heteropolymers that can renature to recognize a given target molecule by Pande (1994)
  81. {'key': '10.1006/jmbi.2000.4422_BIB81', 'series-title': 'Statistical Mechanics', 'author': 'Pathria', 'year': '1996'} / Statistical Mechanics by Pathria (1996)
  82. 10.1016/0022-2836(87)90358-5 / J. Mol. Biol / Tertiary templates for proteins by Ponder (1987)
  83. 10.1021/bi00405a042 / Biochemistry / Comparing the polarities of the amino acids by Radzicka (1988)
  84. 10.1110/ps.9.6.1106 / Protein Sci / Prediction of amino acid sequence from structure by Raha (2000)
  85. 10.1103/PhysRevE.50.1303 / Phys. Rev. ser. E / Statistical mechanics of proteins with “evolutionary selected” sequences by Ramanathan (1994)
  86. 10.1126/science.3388019 / Science / Combinatorial cassette mutagenesis as a probe of the informational contetn of protein sequences by Reidhaar Olson (1988)
  87. 10.1093/protein/5.7.625 / Protein Eng / A new approach to the design of a sequence with the highest affinity for a molecular surface by Reva (1992)
  88. 10.1146/annurev.bb.06.060177.001055 / Annu. Rev. Biophys. Bioeng / Areas, volumes, packing, and protein structure by Richards (1977)
  89. 10.1038/nsb1097-805 / Nature Struct. Biol / Functional rapidly folding proteins from simplified amino acid sequences by Riddle (1997)
  90. 10.1126/science.4023714 / Science / Hydrophobicity of amino acid residues in globular proteins by Rose (1985)
  91. 10.1002/pro.5560071111 / Protein Sci / Stabilizing the subtilisin bpn pro-domain by phage display selection, how restrictive is the amino acid code fox maximum protein stability? by Ruan (1998)
  92. 10.1002/prot.340090107 / Proteins: Struct. Funct. Genet / Database of homology-derived protein structures and the structural meaning of sequence alignment by Sander (1991)
  93. 10.1016/S1359-0278(96)00015-6 / Fold. Des / Protein folding from a combinatorial perspective by Sauer (1996)
  94. 10.1021/jp971707j / J. Phys. Chem. B / Statistical mechanics of the combinatorial synthesis and analysis of folding macromolecules by Saven (1997)
  95. 10.1021/bi9625758 / Biochemistry / Kinetics of folding of the IgG binding domain of peptostreptoccocal protein L by Scalley (1997)
  96. 10.1038/nsb1297-1039 / Nature Struct. Biol / A designed four-helix bundle protein with native-like structure by Schafmeister (1997)
  97. 10.1006/jmbi.1993.1172 / J. Mol. Biol / Rotamers by Schrauber (1993)
  98. 10.1103/PhysRevLett.77.1901 / Phys. Rev. Letters / Optimal protein design procedure by Seno (1996)
  99. 10.1016/S1359-0278(98)00021-2 / Fold. Des / Protein design by Shakhnovich (1998)
  100. 10.1093/protein/6.8.793 / Protein Eng / A new approach to the design of stable proteins by Shakhnovich (1993)
  101. 10.1016/S0022-2836(05)80269-4 / J. Mol. Biol / Calculation of conformational ensembles from potentials of mean force by Sippl (1990)
  102. 10.1063/1.470610 / J. Chem. Phys / Kinetic and thermodynamic analysis of proteinlike heteropolymers by Socci (1995)
  103. 10.1016/S1359-0278(98)00036-4 / Fold. Des / Pairwise calculation of protein solvent-accessible surface areas by Street (1998)
  104. 10.1002/pro.5560060810 / Protein Sci / Coupling backbone flexibility and amino acid sequnece selection in protein design by Su (1997)
  105. 10.1016/0022-2836(87)90520-1 / J. Mol. Biol / Analysis of side-chain orientations in homologous proteins by Summers (1987)
  106. 10.1093/protein/8.12.1205 / Protein Eng / Designing amino acid sequences to fold with good hydrophobic cores by Sun (1995)
  107. 10.1002/pro.5560031220 / Protein Sci / Determinants of protein side-chain packing by Tanimura (1994)
  108. {'key': '10.1006/jmbi.2000.4422_BIB108', 'series-title': 'Statistical Physics 1. Equilibrium Statistical Mechanics', 'author': 'Toda', 'year': '1991'} / Statistical Physics 1. Equilibrium Statistical Mechanics by Toda (1991)
  109. 10.1080/07391102.1991.10507882 / J. Biomol. Struct. Dynam / A new approach to the rapid determination of protein side-chain conformations by Tuffery (1991)
  110. 10.1093/protein/10.4.361 / Protein Eng / Prediction of protein side chain conformations; a study on the influence of backbone accuracy on conformation stability in the rotamer space by Tuffery (1997)
  111. 10.1002/bip.360360106 / Biopolymers / An evaluation of discrete and continuum search techniques for conformational analysis of side-chains in proteins by Vasquez (1995)
  112. 10.1006/jmbi.2000.3758 / J. Mol. Biol / Trading accuracy for speed by Voigt (2000)
  113. 10.1073/pnas.96.10.5486 / Proc. Natl Acad. Sci. USA / Solution structure and dynamics of a de novo designed three-helix bundle protein by Walsh (1999)
  114. 10.1021/ja00315a051 / J. Am. Chem. Soc / A new force field for molecular mechanical simulation of nucleic acids and proteins by Weiner (1984)
  115. 10.1021/bi00064a023 / Biochemistry / Proton muclear magnetic resonance sequential assignments and secondary structure of an immunoglobulin light chain-binding domain of protein L by Wikström (1993)
  116. 10.1021/bi00251a008 / Biochemistry / Three-dimensional solution structure of an immunoglobulin light chain-binding domain of protein L. Comparison with the IgG-binding domains of protein G by Wikström (1994)
  117. 10.1006/jmbi.1995.0364 / J. Mol. Biol / Mapping of the immunoglobulin light chain-binding site of protein L by Wikström (1995)
  118. 10.1073/pnas.92.14.6349 / Proc Natl Acad. Sci. USA / Periodicity of polar and nonpolar amino acids is the major determinant of secondary structure in self-assembling oligomeric peptides by Xiong (1995)
  119. 10.1006/jmbi.1999.3426 / J. Mol. Biol / Statistical theory of combinatorial libraries of folding proteins by Zou (2000)
Dates
Type When
Created 22 years, 11 months ago (Sept. 18, 2002, 3:24 p.m.)
Deposited 4 years, 3 months ago (May 3, 2021, 1:12 a.m.)
Indexed 9 months, 1 week ago (Nov. 19, 2024, 10:35 a.m.)
Issued 24 years, 6 months ago (Feb. 1, 2001)
Published 24 years, 6 months ago (Feb. 1, 2001)
Published Print 24 years, 6 months ago (Feb. 1, 2001)
Funders 0

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@article{Kono_2001, title={Statistical theory for protein combinatorial libraries. packing interactions, backbone flexibility, and the sequence variability of a main-chain structure11Edited by J. Thornton}, volume={306}, ISSN={0022-2836}, url={http://dx.doi.org/10.1006/jmbi.2000.4422}, DOI={10.1006/jmbi.2000.4422}, number={3}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Kono, Hidetoshi and Saven, Jeffery G.}, year={2001}, month=feb, pages={607–628} }