9 papers · ranked by Valyu relevance
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Proteolysis-targeting chimeras (PROTACs) are heterobifunctional molecules composed of an E3 ligase ligand, a linker, and a warhead targeting a protein of interest. Despite their modular structure, accurately identifying and annotating these components in PROTACs is challenging and typically relies on manual curation…
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Fragment-based quantum chemistry offer a means to circumvent the nonlinear computational scaling of conventional electronic structure calculations by partitioning a large calculation into smaller subsystems, then considering the many-body interactions between them. Variants of this approach have been used to…
Gunther Schadow, Yulia Borodina, Victorien Delannée, Wolf-Dietrich Ihlenfeldt + 2 more
There are numerous formats and data models for describing reaction-related data. However, each offers only a limited coverage of the multitude of information that can be of interest to a broad user base in the context of chemical reactions. Structured Product Labeling (SPL) is a robust yet fairly light public XML…
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Today, machine learning models are employed extensively to predict the physicochemical and biological properties of molecules. Their performance is typically evaluated on in-distribution (ID) data, i.e., data originating from the same distribution as the training data. However, the real-world applications of such…
Naveen Malik, Tatyana Bendikov, Michal Lahav, Milko van der Boom
We describe two different functionalities of one metallo-organic film assembled on the surface of a transparent metal-oxide electrode. Two redox-active elements, electrochromic iron-polypyridyl complexes and catalytically-active palladium centers, operate by applying different potentials in aqueous solutions. The color…
Matthew Witman, Peter Schindler
Machine learning (ML) models in the materials sciences that are validated by overly simplistic cross-validation (CV) protocols can yield biased performance estimates for downstream modeling or materials screening tasks. This can be particularly counterproductive for applications where the time and cost of failed…
Felix Bänsch, Jonas Schaub, Betül Sevindik, Samuel Behr + 3 more
Developing and implementing computational algorithms for the extraction of specific substructures from molecular graphs (in silico molecule fragmentation) is an iterative process. It involves repeated sequences of implementing a rule set, applying it to relevant structural data, checking the results, and adjusting the…
Trevor Gokey, David L. Mobley
Molecular mechanics force fields require a chemical perception model to assign parameters to molecules. A recent advancement in force fields is the use of the SMARTS substructure query language as the perception model. Although it is straightforward to write SMARTS patterns to define new force field parameters, it is…
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The two key parameters extracted from Mössbauer spectroscopy, the isomer shift and the quadrupole splitting, have well-known temperature dependencies. While the values’ increase or decrease with sample temperature have long been established, the microscopic origins are less clear. For quantum chemical calculations –…