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Nucleic acids research
Jan 6, 2025
BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, trai...
Bioinformatics (Oxford, England)
Nov 28, 2024
MOTIVATION: RNA is implicated in numerous aberrant cellular functions and disease progressions, highlighting the crucial importance of RNA-targeted drugs. To accelerate the discovery of such drugs, it is essential to develop an effective computationa...
Briefings in bioinformatics
Sep 23, 2024
In this paper, we propose DGCL, a dual-graph neural networks (GNNs)-based contrastive learning (CL) integrated with mixed molecular fingerprints (MFPs) for molecular property prediction. The DGCL-MFP method contains two stages. In the first pretraini...
Nucleic acids research
Jul 5, 2024
Evaluating pharmacokinetic properties of small molecules is considered a key feature in most drug development and high-throughput screening processes. Generally, pharmacokinetics, which represent the fate of drugs in the human body, are described fro...
Bioinformatics (Oxford, England)
Jul 1, 2024
MOTIVATION: The emergence of large chemical repositories and combinatorial chemical spaces, coupled with high-throughput docking and generative AI, have greatly expanded the chemical diversity of small molecules for drug discovery. Selecting compound...
Protein science : a publication of the Protein Society
Jun 1, 2024
The identification of an effective inhibitor is an important starting step in drug development. Unfortunately, many issues such as the characterization of protein binding sites, the screening library, materials for assays, etc., make drug screening a...
Clinical and translational science
May 1, 2024
Accurate prediction of a new compound's pharmacokinetic (PK) profile is pivotal for the success of drug discovery programs. An initial assessment of PK in preclinical species and humans is typically performed through allometric scaling and mathematic...
Chemical & pharmaceutical bulletin
Jan 1, 2024
Recently, remarkable progress has been achieved in artificial intelligence (AI), including machine learning. Various AI models have been proposed for drug discovery, including the design of small molecules, activity prediction, and three-dimensional ...
Bioinformatics (Oxford, England)
Jan 27, 2022
SUMMARY: Deep learning (DL) can significantly accelerate virtual screening of ultra-large chemical libraries, enabling the evaluation of billions of compounds at a fraction of the computational cost and time required by conventional docking. Here, we...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2022
The use of artificial intelligence methods in drug safety began in the early 2000s with applications such as predicting bacterial mutagenicity and hERG inhibition. The field has been endlessly expanding ever since and the models have become more comp...