CONTEXT: The extensive conformational space of flexible molecules poses a significant challenge for predicting chemical reactivity through quantum chemical methods. For curcumin, whose keto-enol tautomerization is crucial to its biological activity a...
Journal of chemical information and modeling
Nov 13, 2025
Heterobifunctional degraders, a class of targeted protein degraders (TPDs), often occupy beyond-rule-of-five (bRo5) chemical space, where traditional passive permeability models─calibrated on drug-like molecules or peptides and based on topological d...
Journal of chemical information and modeling
Oct 9, 2025
In this work, we introduce an automated methodology for the efficient and relatively inexpensive exploration of large high-dimensional chemical spaces, with particular focus on number-of-atoms-conserving processes, such as in mechanochemical reaction...
Journal of chemical information and modeling
Sep 26, 2025
While line notation schemes for molecular structure are well developed, they are generally unable to distinguish different conformations of the same molecule. CSMILES, an extension to the ubiquitous line notation scheme, SMILES, has been developed to...
Journal of chemical information and modeling
Sep 3, 2025
Existing methods for adsorption energy prediction primarily focus on individual molecules or static molecular pairs, lacking the capabilities to model the diverse spatial configurations found in complex solution systems. While traditional data sets a...
Journal of chemical information and modeling
Aug 7, 2025
We present a machine learning model for high-throughput energetic ranking of charged molecular conformers. Based on the ConfRank (Hölzer et al. , 8909-8925) approach, the model is trained in a pairwise fashion to predict energy differences for pair...
Journal of chemical information and modeling
Aug 4, 2025
Machine learning (ML) has become a standard tool for the exploration of the chemical space. Much of the performance of such models depends on the chosen database for a given task. Here, this aspect is investigated for "chemical tasks" including the p...
Journal of chemical information and modeling
Jul 25, 2025
To understand the benefits and drawbacks of 3D combinatorial and deep learning generators, a novel benchmark was created focusing on the recreation of important protein-ligand interactions and 3D ligand conformations. Using the BindingMOAD data set w...
Journal of chemical information and modeling
Jul 3, 2025
Synthetic monomycoloyl glycerol (MMG) analogs possess robust immunostimulatory activity and are investigated as adjuvants for subunit vaccines in preclinical and clinical studies. These synthetic lipids consist of a glycerol moiety attached to a cory...
Journal of chemical information and modeling
Jul 2, 2025
Exploring drug-target interactions (DTIs) is crucial for drug discovery. Most existing methods for predicting DTIs rely solely on the linear structures of molecules, such as SMILES or the amino acid sequence. However, these linear features fail to re...
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