Comparative studies of IR spectra of deprotonated serine with classical and thermostated ring polymer molecular dynamics simulations.

Here we report the vibrational spectra of deprotonated serine calculated from the classical molecular dynamics (MD) simulations and thermostated ring-polymer molecular dynamics (TRPMD) simulation with third-order density-functional tight-binding. In our earlier study [Inakollu and Yu, "A systematic benchmarking of computational vibrational spectroscopy with DFTB3: Normal mode analysis and fast Fourier transform dipole autocorrelation function," J. Comput.

Polarisable force fields: what do they add in biomolecular simulations?

The quality of biomolecular simulations critically depends on the accuracy of the force field used to calculate the potential energy of the molecular configurations. Currently, most simulations employ non-polarisable force fields, which describe electrostatic interactions as the sum of Coulombic interactions between fixed atomic charges. Polarisation of these charge distributions is incorporated only in a mean-field manner.

A systematic benchmarking of computational vibrational spectroscopy with DFTB3: Normal mode analysis and fast Fourier transform dipole autocorrelation function.

Computational vibrational spectroscopy serves as an important tool in the interpretation of experimental infrared (IR) spectra. In this article, we present a systematic benchmarking study of DFTB3 with two different computational vibrational spectroscopic methods, based on either normal mode analysis (NMA) or fast Fourier transform dipole autocorrelation function (FT-DAC). The results were compared with experimental data and theoretical calculations with B3LYP/cc-pVTZ.

Boosting virtual screening enrichments with data fusion: coalescing hits from two-dimensional fingerprints, shape, and docking.

Virtual screening is an effective way to find hits in drug discovery, with approaches ranging from fast information-based similarity methods to more computationally intensive physics-based docking methods. However, the best approach to use for a given project is not clear in advance of the screen. In this work, we show that combining results from multiple methods using a standard score (Z-score) can significantly improve virtual screening enrichments over any of the single screening methods.