DOCK 6: Combining techniques to model RNA–small molecule complexes

作者: P. T. Lang , S. R. Brozell , S. Mukherjee , E. F. Pettersen , E. C. Meng

DOI: 10.1261/RNA.1563609

关键词:

摘要: … versions 4 and 5 (clustering-based algorithm), the protein test set success rates were better than RNA … For version 6 (ranking-based sampling algorithm), the RNA test set success rate …

参考文章(47)
Thomas J. Macke, David Case, Modeling Unusual Nucleic Acid Structures ACS Symposium Series. ,vol. 682, pp. 379- 393 ,(1998)
Molecular modeling of nucleic acids American Chemical Society. ,(1997) , 10.1021/BK-1998-0682
Anton V. Filikov, Venkatraman Mohan, Timothy A. Vickers, Richard H. Griffey, P. Dan Cook, Ruben A. Abagyan, Thomas L. James, Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR Journal of Computer-aided Molecular Design. ,vol. 14, pp. 593- 610 ,(2000) , 10.1023/A:1008121029716
J. Andrew Grant, Barry T. Pickup, Anthony Nicholls, A smooth permittivity function for Poisson–Boltzmann solvation methods Journal of Computational Chemistry. ,vol. 22, pp. 608- 640 ,(2001) , 10.1002/JCC.1032
Christophe Guilbert, Thomas L. James, Docking to RNA via Root-Mean-Square-Deviation-Driven Energy Minimization with Flexible Ligands and Flexible Targets Journal of Chemical Information and Modeling. ,vol. 48, pp. 1257- 1268 ,(2008) , 10.1021/CI8000327
Christopher I. Bayly, Piotr Cieplak, Wendy Cornell, Peter A. Kollman, A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model The Journal of Physical Chemistry. ,vol. 97, pp. 10269- 10280 ,(1993) , 10.1021/J100142A004
William L. Jorgensen, Jayaraman Chandrasekhar, Jeffry D. Madura, Roger W. Impey, Michael L. Klein, Comparison of simple potential functions for simulating liquid water The Journal of Chemical Physics. ,vol. 79, pp. 926- 935 ,(1983) , 10.1063/1.445869
Gregory D. Hawkins, Christopher J. Cramer, Donald G. Truhlar, Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium The Journal of Physical Chemistry. ,vol. 100, pp. 19824- 19839 ,(1996) , 10.1021/JP961710N