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RAIChU: automating the visualisation of natural product biosynthesis

https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00898-x

Published: September 3, 2024 00:00

Natural products are molecules that fulfil a range of important ecological functions. Many natural products have been exploited for pharmaceutical and agricultural applications. In contrast to many other speci...

Evaluating the generalizability of graph neural networks for predicting collision cross section

https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00899-w

Published: August 29, 2024 00:00

Ion Mobility coupled with Mass Spectrometry (IM-MS) is a promising analytical technique that enhances molecular characterization by measuring collision cross-section (CCS) values, which are indicative of the m...

BuildAMol: a versatile Python toolkit for fragment-based molecular design

https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00900-6

Published: August 25, 2024 00:00

In recent years computational methods for molecular modeling have become a prime focus of computational biology and cheminformatics. Many dedicated systems exist for modeling specific classes of molecules such...

Deep learning of multimodal networks with topological regularization for drug repositioning

https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00897-y

Published: August 23, 2024 00:00

Computational techniques for drug-disease prediction are essential in enhancing drug discovery and repositioning. While many methods utilize multimodal networks from various biological databases, few integrate...

Automatic molecular fragmentation by evolutionary optimisation

https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00896-z

Published: August 19, 2024 00:00

Molecular fragmentation is an effective suite of approaches to reduce the formal computational complexity of quantum chemistry calculations while enhancing their algorithmic parallelisability. However, the pra...

Democratizing cheminformatics: interpretable chemical grouping using an automated KNIME workflow

https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00894-1

Published: August 16, 2024 00:00

With the increased availability of chemical data in public databases, innovative techniques and algorithms have emerged for the analysis, exploration, visualization, and extraction of information from these da...

Metis: a python-based user interface to collect expert feedback for generative chemistry models

https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00892-3

Published: August 14, 2024 00:00

One challenge that current de novo drug design models face is a disparity between the user’s expectations and the actual output of the model in practical applications. Tailoring models to better align with che...

Geometric deep learning for molecular property predictions with chemical accuracy across chemical space

https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00895-0

Published: August 13, 2024 00:00

Chemical engineers heavily rely on precise knowledge of physicochemical properties to model chemical processes. Despite the growing popularity of deep learning, it is only rarely applied for property predictio...

MolCompass: multi-tool for the navigation in chemical space and visual validation of QSAR/QSPR models

https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00888-z

Published: August 12, 2024 00:00

The exponential growth of data is challenging for humans because their ability to analyze data is limited. Especially in chemistry, there is a demand for tools that can visualize molecular datasets in a conven...