The journal of physical chemistry. B
Aug 15, 2022
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...
Journal of chemical information and modeling
Jul 5, 2022
The principle of least action is the cornerstone of classical mechanics, theory of relativity, quantum mechanics, and thermodynamics. Here, we describe how a neural network (NN) learns to find the trajectory for a Lennard-Jones (LJ) system that maint...
Biomolecules
Jun 29, 2022
Calculation of protein-ligand binding affinity is a cornerstone of drug discovery. Classic implicit solvent models, which have been widely used to accomplish this task, lack accuracy compared to experimental references. Emerging data-driven models, o...
Journal of computational chemistry
Jun 28, 2022
The conductor-like polarizable continuum model (C-PCM), which is a low-cost solvation model, cannot treat characteristic interactions between the solvent and substructure(s) of the solute. Moreover, the error in a charged system is significant. Using...
Scientific data
Jun 7, 2022
Machine learning approaches in drug discovery, as well as in other areas of the chemical sciences, benefit from curated datasets of physical molecular properties. However, there currently is a lack of data collections featuring large bioactive molecu...
Chemistry, an Asian journal
May 30, 2022
Machine learning (ML) approaches have enabled rapid and efficient molecular property predictions as well as the design of new novel materials. In addition to great success for molecular problems, ML techniques are applied to various chemical reaction...
Acta biotheoretica
Apr 28, 2022
This is a digest of how various researchers in biology and astrobiology have explored questions of what defines living organisms-definitions based on functions or structures observed in organisms, or on systems terms, or on mathematical conceptions l...
Journal of chemical theory and computation
Apr 6, 2022
An effective implementation of enhanced sampling algorithms for molecular dynamics simulations requires knowledge of the approximate reaction coordinate describing the relevant mechanisms in the system. In this work, we focus on the recently develop...