J.V. Harzer, B. Hillebrands, et al.
Journal of Magnetism and Magnetic Materials
We applied our recently developed kinetic computational mutagenesis (KCM) approach [L.T. Chong, W.C. Swope, J.W. Pitera, V.S. Pande, Kinetic computational alanine scanning: application to p53 oligomerization, J. Mol. Biol. 357 (3) (2006) 1039-1049] along with the MM-GBSA approach [J. Srinivasan, T.E. Cheatham 3rd, P. Cieplak, P.A. Kollman, D.A. Case, Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices, J. Am. Chem. Soc. 120 (37) (1998) 9401-9409; P.A. Kollman, I. Massova, C.M. Reyes, B. Kuhn, S. Huo, L.T. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D.A. Case, T.E. Cheatham 3rd., Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models, Acc. Chem. Res. 33 (12) (2000) 889-897] to evaluate the effects of all possible missense mutations on dimerization of the oligomerization domain (residues 326-355) of tumor suppressor p53. The true positive and true negative rates for KCM are comparable (within 5%) to those of MM-GBSA, although MM-GBSA is much less computationally intensive when it is applied to a single energy-minimized configuration per mutant dimer. The potential advantage of KCM is that it can be used to directly examine the kinetic effects of mutations. © 2008 Elsevier Inc. All rights reserved.
J.V. Harzer, B. Hillebrands, et al.
Journal of Magnetism and Magnetic Materials
M. Hargrove, S.W. Crowder, et al.
IEDM 1998
Mitsuru Ueda, Hideharu Mori, et al.
Journal of Polymer Science Part A: Polymer Chemistry
G. Will, N. Masciocchi, et al.
Zeitschrift fur Kristallographie - New Crystal Structures