Conformational changes essential for protein function involve transitions through multiple short-lived, high-energy states within the complex free energy landscape. While existing methods, such as Markov State Models and non-Markovian approaches buil...
Reliable prediction of drug solubility in supercritical carbon dioxide (scCO₂) is crucial for the efficient design of pharmaceutical processes, including particle engineering and supercritical fluid-based extraction. Given that experimental determina...
European journal of medicinal chemistry
Nov 16, 2025
The chimera combining the peptide nucleic acids (PNAs) and peptides represent a promising bifunctional strategy by concurrently binding with protein catalytic pocket and its associated RNA template, effectively disrupting protein's function. Conventi...
Journal of chemical information and modeling
Nov 12, 2025
Dispersion-corrected density functional theory (DFT-D) is widely employed to model large molecular systems at an affordable computational cost and to develop machine-learning interatomic potentials (MLIPs), enabling reliable molecular dynamics (MD) s...
Journal of chemical information and modeling
Nov 10, 2025
Accurate prediction of Gibbs activation energies (Δ) for Diels-Alder (DA) reactions remains a critical challenge in computational chemistry, as conventional density functional theory (DFT) methods often fail to consistently achieve chemical accuracy ...
In this work we introduce TorchANI-Amber, an interface for routine molecular dynamics simulations of biomolecular systems using ANI-style machine learning potentials. TochANI-Amber incorporates the ANI neural network potentials into the Amber softwar...
Journal of chemical information and modeling
Oct 17, 2025
The generation and evaluation of chemical reactions remain challenging with limited comprehensive studies addressing these issues. We introduce the ical Reaction () ystematic ssessment of eneration and valuation () framework, an adaptable end-to-end ...
Harmonizing enzyme-support microenvironments to govern thermodynamic interaction landscapes presents a critical yet underexplored frontier in nanobiocatalysis for pathogen detection. Herein, we architecturally engineer mesoporous resorcinol formaldeh...
ConspectusThis Account discusses recent progress and challenges in binding free energy computations, focusing on two classes of enhanced sampling techniques: alchemical transformations and path-based methods. Binding free energy is a crucial metric i...
Journal of chemical information and modeling
Sep 29, 2025
Accurately predicting the impact of point mutations on protein thermodynamic stability is essential for understanding structure-function relationships and guiding protein design. This challenge is particularly acute for transmembrane proteins (TMPs),...
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