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1
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2
Local and collective motions in protein dynamics.
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3
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Adv Biophys. 1984;18:165-90. doi: 10.1016/0065-227x(84)90011-x.
4
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Proc Natl Acad Sci U S A. 1975 Jun;72(6):2002-6. doi: 10.1073/pnas.72.6.2002.
5
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Biochemistry. 1979 Mar 20;18(6):927-42. doi: 10.1021/bi00573a001.
6
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Biochemistry. 1979 Dec 25;18(26):5834-41. doi: 10.1021/bi00593a013.
7
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Proc Natl Acad Sci U S A. 1983 Jul;80(14):4315-9. doi: 10.1073/pnas.80.14.4315.
8
[Computer simulation of protein molecular dynamics].
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9
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9
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本文引用的文献
1
The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain.
Proc Natl Acad Sci U S A. 1951 Apr;37(4):205-11. doi: 10.1073/pnas.37.4.205.
2
Stereochemistry of polypeptide chain configurations.
J Mol Biol. 1963 Jul;7:95-9. doi: 10.1016/s0022-2836(63)80023-6.
3
Energy refinement of hen egg-white lysozyme.
J Mol Biol. 1974 Jan 25;82(3):393-420. doi: 10.1016/0022-2836(74)90599-3.
4
Refinement of the x-ray structure of lysozyme by complete energy minimization.
Biochemistry. 1974 Feb 12;13(4):757-67. doi: 10.1021/bi00701a019.
5
Dynamics of ligand binding to myoglobin.
Biochemistry. 1975 Dec 2;14(24):5355-73. doi: 10.1021/bi00695a021.
6
Role of structural flexibility in conformational calculations. Application to acetylcholine and beta-methylacetylcholine.
J Am Chem Soc. 1975 Nov 26;97(24):6996-7006. doi: 10.1021/ja00857a009.
7
Dynamics of the aromatic amino acid residues in the globular conformation of the basic pancreatic trypsin inhibitor (BPTI). II. Semi-empirical energy calculations.
Biophys Struct Mech. 1976 Aug 23;2(2):159-80. doi: 10.1007/BF00863707.
8
Sidechain torsional potentials and motion of amino acids in porteins: bovine pancreatic trypsin inhibitor.
Proc Natl Acad Sci U S A. 1975 Jun;72(6):2002-6. doi: 10.1073/pnas.72.6.2002.
9
Protein structural fluctuations during a period of 100 ps.
Nature. 1979 Feb 15;277(5697):578. doi: 10.1038/277578a0.
10
Dynamics of ligand binding to heme proteins.
J Mol Biol. 1979 Aug 15;132(3):343-68. doi: 10.1016/0022-2836(79)90265-1.
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