Pharmacophore models are widely used for the identification of promising primary hits in compound large libraries. Recent studies have demonstrated that pharmacophores retrieved from protein-ligand molecular dynamic trajectories outperform a single crystal complex structure. However, number can be enormous, thus, making it computationally inefficient to use all them virtual screening. In this study, we proposed selection distinct representative by removal with identical three-dimensional...

Density functional theory (DFT) is indubitably the most popular and among successful approaches for approximately solving many-electron Schrödinger equation. The level of understanding on part both researchers students using DFT, however, lacking, given availability black-box software. present work addresses this knowledge gap by providing three Jupyter notebooks, easily accessible through Google Colaboratory (GitHub repository: https://github.com/tjz21/DFT_PIB_Code), that provide a short...

Theoretical spectroscopy plays a crucial role in understanding the properties of materials and molecules. One most promising methods for computing optical spectra chromophores embedded complex environments from first principles is cumulant approach, where both (generally anharmonic) vibrational degrees freedom environmental interactions are explicitly accounted for. In this work, we verify capabilities approach describing effect on linear absorption by studying Crystal Violet (CV) different...

Theoretical spectroscopy plays a crucial role in understanding the properties of materials and molecules. One most promising methods for computing optical spectra chromophores embedded complex environments from first principles is cumulant approach, where both (generally anharmonic) vibrational degrees freedom environmental interactions are explicitly accounted for. In this work, we verify capabilities approach describing effect on linear absorption by studying Crystal Violet (CV) different...

Theoretical spectroscopy plays a crucial role in understanding the properties of materials and molecules. One most promising methods for computing optical spectra chromophores embedded complex environments from first principles is cumulant approach, where both (generally anharmonic) vibrational degrees freedom environmental interactions are explicitly accounted for. In this work, we verify capabilities approach describing effect on linear absorption by studying Crystal Violet (CV) different...

We compare two recently developed strategies, implemented in open source software packages, for computing linear optical spectra condensed phase environments the presence of nonadiabatic effects. Both approaches rely on excitation energy and transition dipole fluctuations along molecular dynamics (MD) trajectories, treating environmental degrees freedom same footing. Spectra are then generated ways: Gaussian non-Condon theory, response functions computed terms independent adiabatic excited...

We outline a computational workflow to model linear optical spectra of molecules in complex environments the presence nonadiabatic effects. The approach relies on computing excitation energy and transition dipole fluctuations along molecular dynamics (MD) trajectories, treating environmental degrees freedom same footing. Spectra are then generated following two distinct strategies: In recently developed Gaussian Non-Condon Theory (GNCT), response functions computed terms independent...

Density-Functional Theory (DFT) is indubitably the most popular and among successful approaches for approximately solving many-electron Schrödinger equation. The level of understanding on part both researchers students using DFT, however, lacking given availability black box software. present work addresses this knowledge gap by providing three Jupyter notebooks, easily accessible through Google Colaboratory (GitHub repository: https://github.com/tjz21/DFT_PIB_Code), that provide a short...