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Structure-constrained molecular generation is a promising approach to drug discovery. The goal of structure-constrained molecular generation is to produce a novel molecule that is similar to a given source mol...
The field of high-resolution mass spectrometry (HRMS) and ancillary hyphenated techniques comprise a rapidly expanding and evolving area. As popularity of HRMS instruments grows, there is a concurrent need for...
Modern computer-assisted synthesis planning tools provide strong support for this problem. However, they are still limited by computational complexity. This limitation may be overcome by scoring the synthetic ...
Ubiquitin-specific-processing protease 7 (USP7) is a promising target protein for cancer therapy, and great attention has been given to the identification of USP7 inhibitors. Traditional virtual screening meth...
Activity cliffs (AC) are formed by pairs of structural analogues that are active against the same target but have a large difference in potency. While much of our knowledge about ACs has originated from the an...
With the ongoing rapid growth of publicly available ligand–protein bioactivity data, there is a trove of valuable data that can be used to train a plethora of machine-learning algorithms. However, not all data...
Explainable artificial intelligence (XAI) methods have shown increasing applicability in chemistry. In this context, visualization techniques can highlight regions of a molecule to reveal their influence over ...
Developing and implementing computational algorithms for the extraction of specific substructures from molecular graphs (in silico molecule fragmentation) is an iterative process. It involves repeated sequence...
Traditional Chinese Medicine (TCM) has been widely used in the treatment of various diseases for millennia. In the modernization process of TCM, TCM ingredient databases are playing more and more important rol...
The relationships between molecular structures and their properties are subtle and complex, and the properties of odor are no exception. Molecules with similar structures, such as a molecule and its optical is...
This article demonstrates how to create Chemical Space Networks (CSNs) using a Python RDKit and NetworkX workflow. CSNs are a type of network visualization that depict compounds as nodes connected by edges, de...
A de novo molecular design workflow can be used together with technologies such as reinforcement learning to navigate the chemical space. A bottleneck in the workflow that remains to be solved is how to integr...
Homologous series are groups of related compounds that share the same core structure attached to a motif that repeats to different degrees. Compounds forming homologous series are of interest in multiple domai...
Deep learning (DL) and machine learning contribute significantly to basic biology research and drug discovery in the past few decades. Recent advances in DL-based generative models have led to superior develop...
In this paper, a reinforcement learning model is proposed that can maximize the predicted binding affinity between a generated molecule and target proteins. The model used to generate molecules in the proposed...
We report the main conclusions of the first Chemoinformatics and Artificial Intelligence Colloquium, Mexico City, June 15–17, 2022. Fifteen lectures were presented during a virtual public event with speakers f...
The joint use of multiple drugs may cause unintended drug-drug interactions (DDIs) and result in adverse consequence to the patients. Accurate identification of DDI types can not only provide hints to avoid th...
While in the last years there has been a dramatic increase in the number of available bioassay datasets, many of them suffer from extremely imbalanced distribution between active and inactive compounds. Thus, ...
The concept of molecular scaffolds as defining core structures of organic molecules is utilised in many areas of chemistry and cheminformatics, e.g. drug design, chemical classification, or the analysis of hig...
Establishing a data-driven pipeline for the discovery of novel materials requires the engineering of material features that can be feasibly calculated and can be applied to predict a material’s target properti...
Prostate cancer is the most common type of cancer in men. The disease presents good survival rates if treated at the early stages. However, the evolution of the disease in its most aggressive variant remains w...
The original article was published in Journal of Cheminformatics 2022 14:67
As an important member of ion channels family, the voltage-gated sodium channel (VGSC/Nav) is associated with a variety of diseases, including epilepsy, migraine, ataxia, etc., and has always been a hot target fo...
G protein-coupled receptors are involved in many biological processes, relaying the extracellular signal inside the cell. Signaling is regulated by the interactions between receptors and their ligands, it can ...
DrugTax is an easy-to-use Python package for small molecule detailed characterization. It extends a previously explored chemical taxonomy making it ready-to-use in any Artificial Intelligence approach. DrugTax...
We report a novel approach for grading chemical structure drawings for remote teaching, integrated into the Moodle platform. Typically, existing online platforms use a binary grading system, which often fails ...
Molecular property prediction (MPP) is vital in drug discovery and drug reposition. Deep learning-based MPP models capture molecular property-related features from various molecule representations. In this pap...
Graph Convolutional Neural Network (GCNN) is a popular class of deep learning (DL) models in material science to predict material properties from the graph representation of molecular structures. Training an a...
Collecting labeled data for many important tasks in chemoinformatics is time consuming and requires expensive experiments. In recent years, machine learning has been used to learn rich representations of molec...
A plethora of AI-based techniques now exists to conduct de novo molecule generation that can devise molecules conditioned towards a particular endpoint in the context of drug design. One popular approach is us...
Virtual screening has significantly improved the success rate of early stage drug discovery. Recent virtual screening methods have improved owing to advances in machine learning and chemical information. Among...
The Correction to this article has been published in Journal of Cheminformatics 2022 14:76
TUCAN is a canonical serialization format that is independent of domain-specific concepts of structure and bonding. The atomic number is the only chemical feature that is used to derive the TUCAN format. Other...
Deep learning has demonstrated promising results in de novo drug design. Often, the general pipeline consists of training a generative model (G) to learn the building rules of valid molecules, then using a bia...
The majority of primary and secondary metabolites in nature have yet to be identified, representing a major challenge for metabolomics studies that currently require reference libraries from analyses of authen...
Compound structure identification is using increasingly more sophisticated computational tools, among which machine learning tools are a recent addition that quickly gains in importance. These tools, of which ...
Extraction of chemical formulas from images was not in the top priority of Computer Vision tasks for a while. The complexity both on the input and prediction sides has made this task challenging for the conven...
Deep learning methods, such as reaction prediction and retrosynthesis analysis, have demonstrated their significance in the chemical field. However, the de novo generation of novel reactions using artificial i...
The related problems of chemical reaction optimization and reaction scope search concern the discovery of reaction pathways and conditions that provide the best percentage yield of a target product. The space ...
Detecting macromolecular (e.g., protein) cavities where small molecules bind is an early step in computer-aided drug discovery. Multiple pocket-detection algorithms have been developed over the past several de...
Management of nanomaterials and nanosafety data needs to operate under the FAIR (findability, accessibility, interoperability, and reusability) principles and this requires a unique, global identifier for each...
Protein mutations occur frequently in biological systems, which may impact, for example, the binding of drugs to their targets through impairing the critical H-bonds, changing the hydrophobic interactions, etc...
Application of chemical named entity recognition (CNER) algorithms allows retrieval of information from texts about chemical compound identifiers and creates associations with physical–chemical properties and ...
Machine learning (ML) models require an extensive, user-driven selection of molecular descriptors in order to learn from chemical structures to predict actives and inactives with a high reliability. In additio...
The original article was published in Journal of Cheminformatics 2022 14:40
Recently, graph neural networks (GNNs) have revolutionized the field of chemical property prediction and achieved state-of-the-art results on benchmark data sets. Compared with the traditional descriptor- and ...
In virtual screening for drug discovery, hit enrichment curves are widely used to assess the performance of ranking algorithms with regard to their ability to identify early enrichment. Unfortunately, research...
Polypharmacy refers to the administration of multiple drugs on a daily basis. It has demonstrated effectiveness in treating many complex diseases , but it has a higher risk of adverse drug reactions. Hence, th...
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