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Conformal prediction has seen many applications in pharmaceutical science, being able to calibrate outputs of machine learning models and producing valid prediction intervals. We here present the open source s...
This paper presents AutoTemplate, an innovative data preprocessing protocol, addressing the crucial need for high-quality chemical reaction datasets in the realm of machine learning applications in organic che...
Generative models have demonstrated substantial promise in Natural Language Processing (NLP) and have found application in designing molecules, as seen in General Pretrained Transformer (GPT) models. In our ef...
Temperature-responsive liquid chromatography (TRLC) offers a promising alternative to reversed-phase liquid chromatography (RPLC) for environmentally friendly analytical techniques by utilizing pure water as a...
Among the various molecular properties and their combinations, it is a costly process to obtain the desired molecular properties through theory or experiment. Using machine learning to analyze molecular struct...
Stereochemistry plays a fundamental role in pharmacology. Here, we systematically investigate the relationship between stereoisomerism and bioactivity on over 1 M compounds, finding that a very significant fra...
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public chemical information resource containing more than 100 million unique chemical structures. One of the most r...
The original article was published in Journal of Cheminformatics 2024 16:48
Identification of interactions between chemical compounds and proteins is crucial for various applications, including drug discovery, target identification, network pharmacology, and elucidation of protein fun...
Accurate ligand binding site prediction (LBSP) within proteins is essential for drug discovery. We developed ProteinUNetResNetV2.0 (PUResNetV2.0), leveraging sparse representation of protein structures to impr...
This study describes the development and evaluation of six new models for predicting physical–chemical (PC) properties that are highly relevant for chemical hazard, exposure, and risk estimation: solubility (i...
Generative models are undergoing rapid research and application to de novo drug design. To facilitate their application and evaluation, we present MolScore. MolScore already contains many drug-design-relevant ...
Drug discovery is an intricate and costly process. Repurposing existing drugs and active compounds offers a viable pathway to develop new therapies for various diseases. By leveraging publicly available biomed...
In drug discovery, virtual screening is crucial for identifying potential hit compounds. This study aims to present a novel pipeline that employs machine learning models that amalgamates various conventional s...
Small molecule identification is a crucial task in analytical chemistry and life sciences. One of the most commonly used technologies to elucidate small molecule structures is mass spectrometry. Spectral libra...
Selecting greener solvents during experiment design is imperative for greener chemistry. While many solvent selection guides are currently used in the pharmaceutical industry, these are often paper-based guide...
De novo molecular design is the process of searching chemical space for drug-like molecules with desired properties, and deep learning has been recognized as a promising solution. In this study, I developed an...
Effective visualization of small molecules is paramount in conveying concepts and results in cheminformatics. Scalable vector graphics (SVG) are preferred for creating such visualizations, as SVGs can be easil...
We present an updated overview of the AiZynthFinder package for retrosynthesis planning. Since the first version was released in 2020, we have added a substantial number of new features based on user feedback....
Pretrained deep learning models self-supervised on large datasets of language, image, and graph representations are often fine-tuned on downstream tasks and have demonstrated remarkable adaptability in a varie...
Deep learning models adapted from natural language processing offer new opportunities for the prediction of active compounds via machine translation of sequential molecular data representations. For example, c...
This work presents a proposed extension to the International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) standard that allows the representation of isotopically-resolv...
Molecular fingerprints are indispensable tools in cheminformatics. However, stereochemistry is generally not considered, which is problematic for large molecules which are almost all chiral.
Protein-ligand binding affinity plays a pivotal role in drug development, particularly in identifying potential ligands for target disease-related proteins. Accurate affinity predictions can significantly redu...
Chemical reaction optimization (RO) is an iterative process that results in large, high-dimensional datasets. Current tools allow for only limited analysis and understanding of parameter spaces, making it hard...
As the world grapples with the relentless challenges posed by diseases like malaria, the advent of sophisticated computational tools has emerged as a beacon of hope in the quest for effective treatments. In th...
Adverse Outcome Pathways (AOPs) have been proposed to facilitate mechanistic understanding of interactions of chemicals/materials with biological systems. Each AOP starts with a molecular initiating event (MIE...
Previous studies have shown that the three-dimensional (3D) geometric and electronic structure of molecules play a crucial role in determining their key properties and intermolecular interactions. Therefore, i...
The Correction to this article has been published in Journal of Cheminformatics 2024 16:68
Machine learning is a valuable tool that can accelerate the discovery and design of materials occupying combinatorial chemical spaces. However, the prerequisite need for vast amounts of training data can be pr...
Accurate atom mapping, which establishes correspondences between atoms in reactants and products, is a crucial step in analyzing chemical reactions. In this paper, we present a novel end-to-end approach that f...
In this paper we present a method that allows leveraging 3D electron density information to train a deep neural network pipeline to segment regions of high, medium and low electronegativity and classify substa...
Protein kinases become an important source of potential drug targets. Developing new, efficient, and safe small-molecule kinase inhibitors has become an important topic in the field of drug research and develo...
Multiple metrics are used when assessing and validating the performance of quantitative structure–activity relationship (QSAR) models. In the case of binary classification, balanced accuracy is a metric to ass...
Wiswesser Line Notation (WLN) is a old line notation for encoding chemical compounds for storage and processing by computers. Whilst the notation itself has long since been surpassed by SMILES and InChI, distr...
Drug combination therapies have shown promise in clinical cancer treatments. However, it is hard to experimentally identify all drug combinations for synergistic interaction even with high-throughput screening...
Poly ADP-ribose polymerase 1 (PARP1) is an attractive therapeutic target for cancer treatment. Machine-learning scoring functions constitute a promising approach to discovering novel PARP1 inhibitors. Cutting-...
Stakeholders of machine learning models desire explainable artificial intelligence (XAI) to produce human-understandable and consistent interpretations. In computational toxicity, augmentation of text-based mo...
Accurate prediction of the enzyme comission (EC) numbers for chemical reactions is essential for the understanding and manipulation of enzyme functions, biocatalytic processes and biosynthetic planning. A numb...
The challenge of devising pathways for organic synthesis remains a central issue in the field of medicinal chemistry. Over the span of six decades, computer-aided synthesis planning has given rise to a plethor...
DGet! is an open-source analysis package written in Python for calculating the degree of deuterium enrichment in isotopically labelled molecules using mass spectrometric data. The nuclear properties of deuteri...
Natural products are a diverse class of compounds with promising biological properties, such as high potency and excellent selectivity. However, they have different structural motifs than typical drug-like com...
Kinetic process models are widely applied in science and engineering, including atmospheric, physiological and technical chemistry, reactor design, or process optimization. These models rely on numerous kineti...
We present a user-friendly molecular generative pipeline called Pocket Crafter, specifically designed to facilitate hit finding activity in the drug discovery process. This workflow utilized a three-dimensiona...
Protein-ligand binding site prediction is a useful tool for understanding the functional behaviour and potential drug-target interactions of a novel protein of interest. However, most binding site prediction m...
In materials science, accurately computing properties like viscosity, melting point, and glass transition temperatures solely through physics-based models is challenging. Data-driven machine learning (ML) also...
Membrane permeability is an in vitro parameter that represents the apparent permeability (Papp) of a compound, and is a key absorption, distribution, metabolism, and excretion parameter in drug development. Al...
Chemical structure segmentation constitutes a pivotal task in cheminformatics, involving the extraction and abstraction of structural information of chemical compounds from text-based sources, including patent...
Computational methods such as molecular docking or molecular dynamics (MD) simulations have been developed to simulate and explore the interactions between biomolecules. However, the interactions obtained usin...
For understanding a chemical compound’s mechanism of action and its side effects, as well as for drug discovery, it is crucial to predict its possible protein targets. This study examines 15 developed target-c...
Autoencoders are frequently used to embed molecules for training of downstream deep learning models. However, evaluation of the chemical information quality in the latent spaces is lacking and the model archit...
