Qiang Cui

TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.

TL;DR: The present study combines earlier extensions and improves them consistently with, first, an improved Coulomb interaction between atomic partial charges, and second, the complete third-order expansion of the DFT total energy, leading to the next generation of theDFTB methodology called DFTB3, which substantially improves the description of charged systems containing elements C, H, N, O, and P.

TL;DR: This review describes the current understanding of allostery, how the mechanisms go beyond the classical MWC/Pauling‐KNF descriptions, and points out that the “new view” of allosteric systems is, in fact, an “old view.”

TL;DR: In this paper, a self-consistent charge density functional tight binding (SCC-DFTB) method was used to obtain the energy of the triosephosphate isomerase (TIM) catalyzed reactions.

TL;DR: Normal mode theory and harmonic potential approximations have been used for all-atom normal mode calculations of large molecular systems using iterative methods as discussed by the authors, using elastic network normal mode analysis.