Journal of chemical theory and computation
May 26, 2023
Cyclic peptides have emerged as a promising class of therapeutics. However, their design remains challenging, and many cyclic peptide drugs are simply natural products or their derivatives. Most cyclic peptides, including the current cyclic peptide ...
Journal of chemical theory and computation
Mar 24, 2023
Finding new enzyme variants with the desired substrate scope requires screening through a large number of potential variants. In a typical enzyme engineering workflow, it is possible to scan a few thousands of variants, and gather several candidates...
Journal of chemical theory and computation
Feb 23, 2023
Kinase drug selectivity is the ground challenge in cancer research. Due to the structurally similar kinase drug pockets, off-target inhibitor toxicity has been a major cause for clinical trial failures. The pockets are similar but not identical. Here...
Journal of chemical theory and computation
Nov 1, 2022
We present two machine learning methodologies that are capable of predicting diffusion Monte Carlo (DMC) energies with small data sets (≈60 DMC calculations in total). The first uses voxel deep neural networks (VDNNs) to predict DMC energy densities ...
Journal of chemical theory and computation
Oct 2, 2022
The machine learning approaches are applied in the dynamical simulation of open quantum systems. The long short-term memory recurrent neural network (LSTM-RNN) models are used to simulate the long-time quantum dynamics, which are built based on the k...
Journal of chemical theory and computation
Sep 27, 2022
The ongoing integration of quantum chemistry, statistical mechanics, and artificial intelligence is paving the route toward more effective and accurate strategies for the investigation of the spectroscopic properties of medium-to-large size chromopho...
Journal of chemical theory and computation
Sep 19, 2022
Leveraging ab initio data at scale has enabled the development of machine learning models capable of extremely accurate and fast molecular property prediction. A central paradigm of many previous studies focuses on generating predictions for only a f...
Journal of chemical theory and computation
Sep 8, 2022
Sampling the minimum energy path (MEP) between two minima of a system is often hindered by the presence of an energy barrier separating the two metastable states. As a consequence, direct sampling based on molecular dynamics or Markov Chain Monte Car...
Journal of chemical theory and computation
Aug 8, 2022
We present here the first application of the quantum chemical topology force field FFLUX to condensed matter simulations. FFLUX offers many-body potential energy surfaces learnt exclusively from data using Gaussian process regression. FFLUX also inc...
Journal of chemical theory and computation
Aug 8, 2022
The traditional approach of computational biology consists of calculating molecule properties by using approximate classical potentials. Interactions between atoms are described by an energy function derived from physical principles or fitted to expe...