Physical chemistry chemical physics : PCCP
Mar 8, 2023
The prediction of the free energy (Δ) of binding for protein-protein complexes is of general scientific interest as it has a variety of applications in the fields of molecular and chemical biology, materials science, and biotechnology. Despite its ce...
Current opinion in structural biology
Jan 31, 2023
The successful recent application of machine learning methods to scientific problems includes the learning of flexible and accurate atomic-level force-fields for materials and biomolecules from quantum chemical data. In parallel, the machine learning...
Random Forest (RF) QSPR models were developed with a data set of homolytic bond dissociation energies (BDE) previously calculated by B3LYP/6-311++G(d,p)//DFTB for 2263 sp3C-H covalent bonds. The best set of attributes consisted in 114 descriptors of ...
The journal of physical chemistry letters
Oct 19, 2022
We have trained the Extreme Minimum Learning Machine (EMLM) machine learning model to predict chemical potentials of individual conformers of multifunctional organic compounds containing carbon, hydrogen, and oxygen. The model is able to predict chem...
Journal of chemical information and modeling
Sep 13, 2022
The availability of AlphaFold2 has led to great excitement in the scientific community─particularly among drug hunters─due to the ability of the algorithm to predict protein structures with high accuracy. However, beyond globally accurate protein str...
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 information and modeling
Sep 6, 2022
Among the factors affecting biological processes such as protein folding and ligand binding, hydration, which is represented by a three-dimensional water site distribution function around the protein, is crucial. The typical methods for computing the...
Hydration free energy (HFE) is a key factor in improving protein-ligand binding free energy (BFE) prediction accuracy. The HFE itself can be calculated using the three-dimensional reference interaction model (3D-RISM); however, the BFE predictions so...
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...
Journal of chemical theory and computation
Jul 11, 2022
Accurate thermochemistry is essential in many chemical disciplines, such as astro-, atmospheric, or combustion chemistry. These areas often involve fleetingly existent intermediates whose thermochemistry is difficult to assess. Whenever direct calori...