- Force-Field Representation of Biomolecular Systems

David N.J. White, A computationally efficient alternative to the Buckingham potential for molecular mechanics calculations. Journal of Computer-aided Molecular Design. ,vol. 11, pp. 517- 521 ,(1997) , 10.1023/A:1007911511862

Xibing He, Pedro E. M. Lopes, Alexander D. MacKerell, Polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator. Biopolymers. ,vol. 99, pp. 724- 738 ,(2013) , 10.1002/BIP.22286

Pedro E. M. Lopes, Jing Huang, Jihyun Shim, Yun Luo, Hui Li, Benoît Roux, Alexander D. MacKerell, Force Field for Peptides and Proteins based on the Classical Drude Oscillator. Journal of Chemical Theory and Computation. ,vol. 9, pp. 5430- 5449 ,(2013) , 10.1021/CT400781B

Robert J. Woods, Raymond A. Dwek, Christopher J. Edge, Bert Fraser-Reid, Molecular Mechanical and Molecular Dynamic Simulations of Glycoproteins and Oligosaccharides. 1. GLYCAM_93 Parameter Development The Journal of Physical Chemistry. ,vol. 99, pp. 3832- 3846 ,(1995) , 10.1021/J100011A061

Nicolas Foloppe, Alexander D MacKerell, Jr, None, All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data Journal of Computational Chemistry. ,vol. 21, pp. 86- 104 ,(2000) , 10.1002/(SICI)1096-987X(20000130)21:2<86::AID-JCC2>3.0.CO;2-G

Jihyun Shim, Andrew Coop, Alexander D. MacKerell, Consensus 3D model of μ-opioid receptor ligand efficacy based on a quantitative Conformationally Sampled Pharmacophore. Journal of Physical Chemistry B. ,vol. 115, pp. 7487- 7496 ,(2011) , 10.1021/JP202542G

Thomas A. Halgren, Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules Journal of Computational Chemistry. ,vol. 17, pp. 616- 641 ,(1996) , 10.1002/(SICI)1096-987X(199604)17:5/6<616::AID-JCC5>3.0.CO;2-X

Robert Abel, Tom Young, Ramy Farid, Bruce J Berne, Richard A Friesner, None, Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding Journal of the American Chemical Society. ,vol. 130, pp. 2817- 2831 ,(2008) , 10.1021/JA0771033

Jan Norberg, Lennart Nilsson, Constant pressure molecular dynamics simulations of the dodecamers: d(GCGCGCGCGCGC)2 and r(GCGCGCGCGCGC)2 Journal of Chemical Physics. ,vol. 104, pp. 6052- 6057 ,(1996) , 10.1063/1.471341

Venkata Velvadapu, Ian Glassford, Miseon Lee, Tapas Paul, Charles DeBrosse, Dorota Klepacki, Meagan C. Small, Alexander D. MacKerell, Rodrigo B. Andrade, Desmethyl Macrolides: Synthesis and Evaluation of 4,10-Didesmethyl Telithromycin ACS Medicinal Chemistry Letters. ,vol. 3, pp. 211- 215 ,(2012) , 10.1021/ML200254H