ICFF: a new method to incorporate implicit flexibility into an internal coordinate force field.
作者： Vsevolod Katritch , Maxim Totrov , Ruben Abagyan
DOI: 10.1002/JCC.10091
关键词:
摘要: OAK-B135 ICFF: A New Method to Incorporate Implicit Flexibility into an Internal Coordinate Force Field
osti.gov
sci-hub.se 参考文章(58)
Jean-Yves Trosset, Harold A. Scheraga, FLEXIBLE DOCKING SIMULATIONS : SCALED COLLECTIVE VARIABLE MONTE CARLO MINIMIZATION APPROACH USING BEZIER SPLINES, AND COMPARISON WITH A STANDARD MONTE CARLO ALGORITHM Journal of Computational Chemistry. ,vol. 20, pp. 244- 252 ,(1999) , 10.1002/(SICI)1096-987X(19990130)20:2<244::AID-JCC6>3.0.CO;2-A
Akio Kitao, Nobuhiro Go, Investigating protein dynamics in collective coordinate space. Current Opinion in Structural Biology. ,vol. 9, pp. 164- 169 ,(1999) , 10.1016/S0959-440X(99)80023-2
Tokio Horiuchi, Nobuhiro Gō, Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: human lysozyme. Proteins. ,vol. 10, pp. 106- 116 ,(1991) , 10.1002/PROT.340100204
K.-H. Chen, G.A. Walker, N.L. Allinger, A molecular mechanics (MM3) study of fluorinated hydrocarbons Journal of Molecular Structure-theochem. ,vol. 490, pp. 87- 107 ,(1999) , 10.1016/S0166-1280(99)00079-2
Themis Lazaridis, Martin Karplus, Effective energy functions for protein structure prediction Current Opinion in Structural Biology. ,vol. 10, pp. 139- 145 ,(2000) , 10.1016/S0959-440X(00)00063-4
William L. Jorgensen, David S. Maxwell, Julian Tirado-Rives, Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids Journal of the American Chemical Society. ,vol. 118, pp. 11225- 11236 ,(1996) , 10.1021/JA9621760
Ailan Cheng, Scott A Best, Kenneth M Merz, Charles H Reynolds, GB/SA water model for the Merck molecular force field (MMFF) Journal of Molecular Graphics and Modelling. ,vol. 18, pp. 273- 282 ,(2000) , 10.1016/S1093-3263(00)00038-3
Thomas A. Halgren, MMFF VII. Characterization of MMFF94, MMFF94s, and other widely available force fields for conformational energies and for intermolecular‐interaction energies and geometries Journal of Computational Chemistry. ,vol. 20, pp. 730- 748 ,(1999) , 10.1002/(SICI)1096-987X(199905)20:7<730::AID-JCC8>3.0.CO;2-T
George Nemethy, Kenneth D. Gibson, Kathleen A. Palmer, Chang No. Yoon, Germana Paterlini, Adriana Zagari, Shirley Rumsey, Harold A. Scheraga, Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides The Journal of Physical Chemistry. ,vol. 96, pp. 6472- 6484 ,(1994) , 10.1021/J100194A068
Ruben Abagyan, Maxim Totrov, High-throughput docking for lead generation. Current Opinion in Chemical Biology. ,vol. 5, pp. 375- 382 ,(2001) , 10.1016/S1367-5931(00)00217-9