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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...
Virtual screening (VS) aids in prioritizing unknown bio-interactions between compounds and protein targets for empirical drug discovery. In standard VS exercise, roughly 10% of top-ranked molecules exhibit act...
Comparing chemical structures to infer protein targets and functions is a common approach, but basing comparisons on chemical similarity alone can be misleading. Here we present a methodology for predicting ta...
UDP-glucuronosyltransferases (UGTs) have gained increasing attention as they play important roles in the phase II metabolism of drugs. Due to the time-consuming process and high cost of experimental approaches...
Bitterness is an aversive cue elicited by thousands of chemically diverse compounds. Bitter taste may prevent consumption of foods and jeopardize drug compliance. The G protein-coupled receptors for bitter tas...
Blood–brain barrier is a pivotal factor to be considered in the process of central nervous system (CNS) drug development, and it is of great significance to rapidly explore the blood–brain barrier permeability...
Lignin is an aromatic biopolymer found in ubiquitous sources of woody biomass. Designing and optimizing lignin valorization processes requires a fundamental understanding of lignin structures. Experimental cha...
The original article was published in Journal of Cheminformatics 2022 14:35
Optical chemical structure recognition from scientific publications is essential for rediscovering a chemical structure. It is an extremely challenging problem, and current rule-based and deep-learning methods...
Drug design is an important area of study for pharmaceutical businesses. However, low efficacy, off-target delivery, time consumption, and high cost are challenges and can create barriers that impact this proc...
The Correction to this article has been published in Journal of Cheminformatics 2022 14:53
Predicting transition state geometries is one of the most challenging tasks in computational chemistry, which often requires expert-based knowledge and permanent human intervention. This short communication re...
This commentary provides an overview of the publications in, and the citations to, the first twelve volumes of the Journal of Cheminformatics, covering the period 2009–2020. The analysis is based on the 622 artic...
As an alternative to one drug-one target approaches, systems biology methods can provide a deeper insight into the holistic effects of drugs. Network-based approaches are tools of systems biology, that can rep...
The translation of images of chemical structures into machine-readable representations of the depicted molecules is known as optical chemical structure recognition (OCSR). There has been a lot of progress over...
As efforts to computationally describe and simulate the biochemical world become more commonplace, computer programs that are capable of in silico chemistry play an increasingly important role in biochemical r...
Retention time information is used for metabolite annotation in metabolomic experiments. But its usefulness is hindered by the availability of experimental retention time data in metabolomic databases, and by ...
Recently, imputation techniques have been adapted to predict activity values among sparse bioactivity matrices, showing improvements in predictive performance over traditional QSAR models. These models are abl...
