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The original article was published in Journal of Cheminformatics 2023 15:55
Molecular descriptors characterize the biological, physical, and chemical properties of molecules and have long been used for understanding molecular interactions and facilitating materials design. Some of the...
The original article was published in Journal of Cheminformatics 2023 15:26
Explainable machine learning is increasingly used in drug discovery to help rationalize compound property predictions. Feature attribution techniques are popular choices to identify which molecular substructur...
Metabolomics by gas chromatography/mass spectrometry (GC/MS) provides a standardized and reliable platform for understanding small molecule biology. Since 2005, the West Coast Metabolomics Center at the Univer...
Machine learning has great potential in predicting chemical information with greater precision than traditional methods. Graph neural networks (GNNs) have become increasingly popular in recent years, as they c...
The identification of human proteins that are amenable to pharmacologic modulation without significant off-target effects remains an important unsolved challenge. Computational methods have been devised to ide...
Machine learning-based scoring functions (MLSFs) have shown potential for improving virtual screening capabilities over classical scoring functions (SFs). Due to the high computational cost in the process of f...
Current biological and chemical research is increasingly dependent on the reusability of previously acquired data, which typically come from various sources. Consequently, there is a growing need for database ...
Off-target drug interactions are a major reason for candidate failure in the drug discovery process. Anticipating potential drug’s adverse effects in the early stages is necessary to minimize health risks to p...
The vast size of chemical space necessitates computational approaches to automate and accelerate the design of molecular sequences to guide experimental efforts for drug discovery. Genetic algorithms provide a...
Retrosynthesis is an important task in organic chemistry. Recently, numerous data-driven approaches have achieved promising results in this task. However, in practice, these data-driven methods might lead to s...
Three-dimensional (3D) conformations of a small molecule profoundly affect its binding to the target of interest, the resulting biological effects, and its disposition in living organisms, but it is challengin...
The applicability domain of machine learning models trained on structural fingerprints for the prediction of biological endpoints is often limited by the lack of diversity of chemical space of the training dat...
Tokenization is an important preprocessing step in natural language processing that may have a significant influence on prediction quality. This research showed that the traditional SMILES tokenization has a c...
The Correction to this article has been published in Journal of Cheminformatics 2023 15:70
Accurate prediction of molecular properties is essential in the screening and development of drug molecules and other functional materials. Traditionally, property-specific molecular descriptors are used in ma...
Predicting in advance the behavior of new chemical compounds can support the design process of new products by directing the research toward the most promising candidates and ruling out others. Such predictive...
Metabolomics experiments generate highly complex datasets, which are time and work-intensive, sometimes even error-prone if inspected manually. Therefore, new methods for automated, fast, reproducible, and acc...
We derived and implemented a linear classification algorithm for the prediction of a molecule’s odor, called Olfactory Weighted Sum (OWSum). Our approach relies solely on structural patterns of the molecules a...
Drug resistance represents a major obstacle to therapeutic innovations and is a prevalent feature in prostate cancer (PCa). Androgen receptors (ARs) are the hallmark therapeutic target for prostate cancer modu...
It is insightful to report an estimator that describes how certain a model is in a prediction, additionally to the prediction alone. For regression tasks, most approaches implement a variation of the ensemble ...
Identification and validation of bioactive small-molecule targets is a significant challenge in drug discovery. In recent years, various in-silico approaches have been proposed to expedite time- and resource-cons...
Pairs of similar compounds that only differ by a small structural modification but exhibit a large difference in their binding affinity for a given target are known as activity cliffs (ACs). It has been hypoth...
Descriptor generation methods using latent representations of encoder–decoder (ED) models with SMILES as input are useful because of the continuity of descriptor and restorability to the structure. However, it...
Efficient and machine-readable representations are needed to accurately identify, validate and communicate information of chemical structures. Many such representations have been developed (as, for example, th...
Artificial intelligence has deeply revolutionized the field of medicinal chemistry with many impressive applications, but the success of these applications requires a massive amount of training samples with hi...
Artificial intelligence (AI)-based molecular design methods, especially deep generative models for generating novel molecule structures, have gratified our imagination to explore unknown chemical space without...
The increasing amount of chemical reaction data makes traditional ways to navigate its corpus less effective, while the demand for novel approaches and instruments is rising. Recent data science and machine learn...
Ligand-based virtual screening is a widespread method in modern drug design. It allows for a rapid screening of large compound databases in order to identify similar structures. Here we report an open-source c...
High throughput screening (HTS) is widely used in drug discovery and chemical biology to identify and characterize agents having pharmacologic properties often by evaluation of large chemical libraries. Standa...
Drug discovery for a protein target is a laborious and costly process. Deep learning (DL) methods have been applied to drug discovery and successfully generated novel molecular structures, and they can substan...
Glycans are important polysaccharides on cellular surfaces that are bound to glycoproteins and glycolipids. These are one of the most common post-translational modifications of proteins in eukaryotic cells. Th...
Vibrational circular dichroism (VCD) spectroscopy can generate the data required for the assignment of absolute configuration, but the spectra are hard to interpret. We have recorded VCD data for thirty pairs ...
Chemical mutagenicity is a serious issue that needs to be addressed in early drug discovery. Over a long period of time, medicinal chemists have manually summarized a series of empirical rules for the optimiza...
Toxicological evaluation of substances in regulation still often relies on animal experiments. Understanding the substances’ mode-of-action is crucial to develop alternative test strategies. Omics methods are ...
Drug combination therapies are promising clinical treatments for curing patients. However, efficiently identifying valid drug combinations remains challenging because the number of available drugs has increase...
Mapping the chemical space of compounds to chemical structures remains a challenge in metabolomics. Despite the advancements in untargeted liquid chromatography-mass spectrometry (LC–MS) to achieve a high-thro...
Protein mutations, especially those which occur in the binding site, play an important role in inter-individual drug response and may alter binding affinity and thus impact the drug’s efficacy and side effects...
The original article was published in Journal of Cheminformatics 2023 15:20
Graph convolutional neural networks (GCNs) have been repeatedly shown to have robust capacities for modeling graph data such as small molecules. Message-passing neural networks (MPNNs), a group of GCN variants...
Non-target analysis combined with liquid chromatography high resolution mass spectrometry is considered one of the most comprehensive strategies for the detection and identification of known and unknown chemic...
Existing molecular property prediction methods based on deep learning ignore the generalization ability of the nonlinear representation of molecular features and the reasonable assignment of weights of molecul...
The simplified molecular-input line-entry system (SMILES) is the most prevalent molecular representation used in AI-based chemical applications. However, there are innate limitations associated with the intern...
The Correction to this article has been published in Journal of Cheminformatics 2023 15:68
Published reports of chemical compounds often contain multiple machine-readable descriptions which may supplement each other in order to yield coherent and complete chemical representations. This publication p...
Rational drug design often starts from specific scaffolds to which side chains/substituents are added or modified due to the large drug-like chemical space available to search for novel drug-like molecules. Wi...
The influence of molecular fragmentation and parameter settings on a mesoscopic dissipative particle dynamics (DPD) simulation of lamellar bilayer formation for a C10E4/water mixture is studied. A “bottom-up” dec...
Generative deep learning models have emerged as a powerful approach for de novo drug design as they aid researchers in finding new molecules with desired properties. Despite continuous improvements in the fiel...
