![]() ![]() We also introduce a novel, maximum-likelihood method to parameterize the side chain interactions using protein structures. Our method, termed Upside, employs a reduced model involving the three backbone atoms, along with the carbonyl oxygen and amide proton, and a single (oriented) side chain bead having multiple locations reflecting the conformational diversity of the side chain’s rotameric states. This computation results in extremely rapid equilibration and sampling of the Boltzmann distribution. The side chain free energy is computed on the fly, allowing the protein backbone dynamics to traverse a greatly smoothed energetic landscape. ![]() In analogy with the adiabatic Born-Oppenheimer approximation for electronic structure, the protein backbone dynamics are simulated as preceding according to the dictates of the free energy of an instantaneously-equilibrated side chain potential. To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics, we present a rapid self-consistent approximation of the side chain free energy at every integration step. ![]()
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