Journal of Cheminformatics – Page 2

Prediction of chemical reaction yields with large-scale multi-view pre-training

February 25, 2024February 25, 2024 Runhan Shi, Gufeng Yu, Xiaohong Huo and Yang Yang Edit

Developing machine learning models with high generalization capability for predicting chemical reaction yields is of significant interest and importance. The efficacy of such models depends heavily on the repr...

Ontologies4Cat: investigating the landscape of ontologies for catalysis research data management

February 7, 2024February 7, 2024 Alexander S. Behr, Hendrik Borgelt and Norbert Kockmann Edit

As scientific digitization advances it is imperative ensuring data is Findable, Accessible, Interoperable, and Reusable (FAIR) for machine-processable data. Ontologies play a vital role in enhancing data FAIRn...

DLM-DTI: a dual language model for the prediction of drug-target interaction with hint-based learning

February 1, 2024February 1, 2024 Jonghyun Lee, Dae Won Jun, Ildae Song and Yun Kim Edit

The drug discovery process is demanding and time-consuming, and machine learning-based research is increasingly proposed to enhance efficiency. A significant challenge in this field is predicting whether a dru...

CRAFT: a web-integrated cavity prediction tool based on flow transfer algorithm

January 30, 2024January 30, 2024 Anuj Gahlawat, Anjali Singh, Hardeep Sandhu and Prabha Garg Edit

Numerous computational methods, including evolutionary-based, energy-based, and geometrical-based methods, are utilized to identify cavities inside proteins. Cavity information aids protein function annotation...

Enhancing chemical synthesis: a two-stage deep neural network for predicting feasible reaction conditions

January 24, 2024January 24, 2024 Lung-Yi Chen and Yi-Pei Li Edit

In the field of chemical synthesis planning, the accurate recommendation of reaction conditions is essential for achieving successful outcomes. This work introduces an innovative deep learning approach designe...

IDSL_MINT: a deep learning framework to predict molecular fingerprints from mass spectra

January 18, 2024January 18, 2024 Sadjad Fakouri Baygi and Dinesh Kumar Barupal Edit

The majority of tandem mass spectrometry (MS/MS) spectra in untargeted metabolomics and exposomics studies lack any annotation. Our deep learning framework, Integrated Data Science Laboratory for Metabolomics ...

Structure-based, deep-learning models for protein-ligand binding affinity prediction

January 3, 2024January 3, 2024 Debby D. Wang, Wenhui Wu and Ran Wang Edit

The launch of AlphaFold series has brought deep-learning techniques into the molecular structural science. As another crucial problem, structure-based prediction of protein-ligand binding affinity urgently cal...

InterDILI: interpretable prediction of drug-induced liver injury through permutation feature importance and attention mechanism

January 3, 2024January 3, 2024 Soyeon Lee and Sunyong Yoo Edit

Safety is one of the important factors constraining the distribution of clinical drugs on the market. Drug-induced liver injury (DILI) is the leading cause of safety problems produced by drug side effects. The...

NMR shift prediction from small data quantities

November 27, 2023November 27, 2023 Herman Rull, Markus Fischer and Stefan Kuhn Edit

Prediction of chemical shift in NMR using machine learning methods is typically done with the maximum amount of data available to achieve the best results. In some cases, such large amounts of data are not ava...

An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification

November 23, 2023November 23, 2023 Daniel Probst Edit

Assigning or proposing a catalysing enzyme given a chemical or biochemical reaction is of great interest to life sciences and chemistry alike. The exploration and design of metabolic pathways and the challenge...