(Nazarbayev University, 2014) Balabaev, N. K.; Finkelstein, A. V.; Galzitskaya, O. V.; Garbuzynskiy, S. O.; Glyakina, A. V.; Lobanov, M. Yu.; Matkarimov, B.
Recent progress in modeling of protein folding in Dr. Shaw laboratory has been
achieved only after some improvements of potentials of covalent forces, taken from the standard AMBER
force field; and still, the force field used is not quite satisfactory to reproduce folded structures of some
larger proteins, having significant, about 5A, RMS deviation between the computed and experimentally
determined 3D structures. The objective of this research is to develop and test new polarizable atomic
force fields (FFs) for "in-vacuum" and "in-water" non-bonded interactions based on AMBER ff99SBILDN
force fields, improved by inclusion of new terms. FFs parameter optimization will be done using
our set of molecular crystals with crystallographic data from the Cambridge Structural Database and
sublimation/solvation thermodynamics characteristics from various sources.