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Developing compounds with novel structures is important for the production of new drugs. From an intellectual perspective, confirming the patent status of newly developed compounds is essential, particularly f...
Time-split cross-validation is broadly recognized as the gold standard for validating predictive models intended for use in medicinal chemistry projects. Unfortunately this type of data is not broadly availabl...
The solubility of proteins stands as a pivotal factor in the realm of pharmaceutical research and production. Addressing the imperative to enhance production efficiency and curtail experimental costs, the dema...
While the Protein Data Bank (PDB) contains a wealth of structural information on ligands bound to macromolecules, their analysis can be challenging due to the large amount and diversity of data. Here, we prese...
This paper presents a novel approach called Pharmacophore Activity Delta for extracting outstanding pharmacophores from a chemogenomic dataset, with a specific focus on a kinase target known as BCR-ABL. The me...
The discovery and utilization of natural products derived from endophytic microorganisms have garnered significant attention in pharmaceutical research. While remarkable progress has been made in this field ea...
Prediction of chemical shift in NMR using machine learning methods is typically done with the maximum amount of data available to achieve the best results. In some cases, such large amounts of data are not ava...
Assigning or proposing a catalysing enzyme given a chemical or biochemical reaction is of great interest to life sciences and chemistry alike. The exploration and design of metabolic pathways and the challenge...
While a multitude of deep generative models have recently emerged there exists no best practice for their practically relevant validation. On the one hand, novel de novo-generated molecules cannot be refuted by r...
In chemistry-related disciplines, a vast repository of molecular structural data has been documented in scientific publications but remains inaccessible to computational analyses owing to its non-machine-reada...
BBPs have the potential to facilitate the delivery of drugs to the brain, opening up new avenues for the development of treatments targeting diseases of the central nervous system (CNS). The obstacle faced in ...
The discovery of both distinctive lead molecules and novel drug targets is a great challenge in drug discovery, which particularly accounts for orphan diseases. Huntington’s disease (HD) is an orphan, neurodeg...
The original article was published in Journal of Cheminformatics 2023 15:94
Plants are one of the primary sources of natural products for drug development. However, despite centuries of research, only a limited region of the phytochemical space has been studied. To understand the scop...
Quantifying imperfect symmetry of molecules can help explore the sources, roles and extent of structural distortion. Based on the established methodology of continuous symmetry and chirality measures, we devel...
Deep learning models have proven to be a powerful tool for the prediction of molecular properties for applications including drug design and the development of energy storage materials. However, in order to le...
Identifying the molecular formula and fragmentation reactions of an unknown compound from its mass spectrum is crucial in areas such as natural product chemistry and metabolomics. We propose a method for ident...
With the continuous development of artificial intelligence technology, more and more computational models for generating new molecules are being developed. However, we are often confronted with the question of...
Docking of large compound collections becomes an important procedure to discover new chemical entities. Screening of large sets of compounds may also occur in de novo design projects guided by molecular dockin...
Established molecular machine learning models process individual molecules as inputs to predict their biological, chemical, or physical properties. However, such algorithms require large datasets and have not ...
Science and art have been connected for centuries. With the development of new computational methods, new scientific disciplines have emerged, such as computational chemistry, and related fields, such as chemi...
A reliable and practical determination of a chemical species’ solubility in water continues to be examined using empirical observations and exhaustive experimental studies alone. Predictions of chemical solubi...
In recent years, cheminformatics has experienced significant advancements through the development of new open-source software tools based on various cheminformatics programming toolkits. However, adopting thes...
Compound–protein interactions (CPI) play significant roles in drug development. To avoid side effects, it is also crucial to evaluate drug selectivity when binding to different targets. However, most selectivi...
Gut-targeted drugs provide a new drug modality besides that of oral, systemic molecules, that could tap into the growing knowledge of gut metabolites of bacterial or host origin and their involvement in biolog...
Ultra-large chemical libraries are reaching 10s to 100s of billions of molecules. A challenge for these libraries is to efficiently check if a proposed molecule is present. Here we propose and study Bloom filt...
Metal–organic frameworks (MOFs), are porous crystalline structures comprising of metal ions or clusters intricately linked with organic entities, displaying topological diversity and effortless chemical flexib...
The Correction to this article has been published in Journal of Cheminformatics 2023 15:108
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...
