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In recent years, drug design has been revolutionized by the application of deep learning techniques, and molecule generation is a crucial aspect of this transformation. However, most of the current deep learni...
Computational molecular design can yield chemically unreasonable compounds when performed carelessly. A popular strategy to mitigate this risk is mimicking reference chemistry. This is commonly achieved by res...
Self-supervised neural language models have recently found wide applications in the generative design of organic molecules and protein sequences as well as representation learning for downstream structure clas...
Mass-Suite (MSS) is a Python-based, open-source software package designed to analyze high-resolution mass spectrometry (HRMS)-based non-targeted analysis (NTA) data, particularly for water quality assessment and ...
Machine learning-based chemical screening has made substantial progress in recent years. However, these predictions often have low accuracy and high uncertainty when identifying new active chemical scaffolds. ...
Opioids are essential pharmaceuticals due to their analgesic properties, however, lethal side effects, addiction, and opioid tolerance are extremely challenging. The development of novel molecules targeting the
Many recently proposed structure-based virtual screening models appear to be able to accurately distinguish high affinity binders from non-binders. However, several recent studies have shown that they often do...
Generative models are frequently used for de novo design in drug discovery projects to propose new molecules. However, the question of whether or not the generated molecules can be synthesized is not systemati...
We report the major highlights of the School of Cheminformatics in Latin America, Mexico City, November 24–25, 2022. Six lectures, one workshop, and one roundtable with four editors were presented during an on...
Graph neural networks have recently become a standard method for analyzing chemical compounds. In the field of molecular property prediction, the emphasis is now on designing new model architectures, and the i...
Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging (MALDI-MSI) spatially resolves the chemical composition of tissues. Lipids are of particular interest, as they influence important biologic...
We present pyPept, a set of executables and underlying python-language classes to easily create, manipulate, and analyze peptide molecules using the FASTA, HELM, or recently-developed BILN notations. The frame...
We developed a new seriation merit function for enhancing the visual information of data matrices. A local similarity matrix is calculated, where the average similarity of neighbouring objects is calculated in...
In recent years, the field of computational drug design has made significant strides in the development of artificial intelligence (AI) models for the generation of de novo chemical compounds with desired prop...
Lipophilicity is a fundamental physical property that significantly affects various aspects of drug behavior, including solubility, permeability, metabolism, distribution, protein binding, and toxicity. Accura...
Siamese networks, representing a novel class of neural networks, consist of two identical subnetworks sharing weights but receiving different inputs. Here we present a similarity-based pairing method for gener...
Proteochemometric (PCM) modelling is a powerful computational drug discovery tool used in bioactivity prediction of potential drug candidates relying on both chemical and protein information. In PCM features a...
Decision tree ensembles are among the most robust, high-performing and computationally efficient machine learning approaches for quantitative structure–activity relationship (QSAR) modeling. Among them, gradie...
In recent years, it has been seen that artificial intelligence (AI) starts to bring revolutionary changes to chemical synthesis. However, the lack of suitable ways of representing chemical reactions and the sc...
The identification of molecular structure is essential for understanding chemical diversity and for developing drug leads from small molecules. Nevertheless, the structure elucidation of small molecules by Nuc...
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...
