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本文引用的文献
1
Some factors in the interpretation of protein denaturation.
Adv Protein Chem. 1959;14:1-63. doi: 10.1016/s0065-3233(08)60608-7.
2
Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation.
J Mol Biol. 1997 Feb 14;266(1):195-214. doi: 10.1006/jmbi.1996.0758.
3
What makes a protein a protein? Hydrophobic core designs that specify stability and structural properties.
Protein Sci. 1996 Aug;5(8):1584-93. doi: 10.1002/pro.5560050813.
4
Mobile unnatural amino acid side chains in the core of staphylococcal nuclease.
Protein Sci. 1996 Jun;5(6):1026-31. doi: 10.1002/pro.5560050605.
5
Constructing lattice models of protein chains with side groups.
J Comput Biol. 1995 Winter;2(4):527-35. doi: 10.1089/cmb.1995.2.527.
6
Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.
J Mol Biol. 1996 Mar 1;256(3):623-44. doi: 10.1006/jmbi.1996.0114.
7
Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets.
Protein Sci. 1995 Oct;4(10):2107-17. doi: 10.1002/pro.5560041016.
8
An empirical energy function for threading protein sequence through the folding motif.
Proteins. 1993 May;16(1):92-112. doi: 10.1002/prot.340160110.
9
Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies.
Protein Eng. 1993 Nov;6(8):811-20. doi: 10.1093/protein/6.8.811.
10
The crystal structure of a mutant protein with altered but improved hydrophobic core packing.
Proc Natl Acad Sci U S A. 1994 Jan 4;91(1):423-7. doi: 10.1073/pnas.91.1.423.
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