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本文引用的文献
1
All-atom empirical potential for molecular modeling and dynamics studies of proteins.
J Phys Chem B. 1998 Apr 30;102(18):3586-616. doi: 10.1021/jp973084f.
2
Implicit solvent models.
Biophys Chem. 1999 Apr 5;78(1-2):1-20. doi: 10.1016/s0301-4622(98)00226-9.
3
Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction.
Proteins. 2004 Aug 15;56(3):475-86. doi: 10.1002/prot.20133.
4
An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state.
Protein Sci. 2004 Feb;13(2):400-11. doi: 10.1110/ps.03348304.
5
Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential.
Protein Sci. 2004 Feb;13(2):391-9. doi: 10.1110/ps.03411904.
6
A graph-theory algorithm for rapid protein side-chain prediction.
Protein Sci. 2003 Sep;12(9):2001-14. doi: 10.1110/ps.03154503.
7
On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy.
J Am Chem Soc. 2003 Aug 6;125(31):9523-30. doi: 10.1021/ja029833a.
8
Protocol for MM/PBSA molecular dynamics simulations of proteins.
Biophys J. 2003 Jul;85(1):159-66. doi: 10.1016/S0006-3495(03)74462-2.
9
Amino acid empirical contact energy definitions for fold recognition in the space of contact maps.
BMC Bioinformatics. 2003 Feb 28;4:8. doi: 10.1186/1471-2105-4-8.
10
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. 2003 Apr 1;51(1):21-40. doi: 10.1002/prot.10235.
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