Ascorbate: a forgotten component in the cytotoxicity of Cu(II) ATCUN peptide complexes.

In 1983, Linus Pauling and colleagues reported about enhanced antitumor activity of the Cu(II) complex of the simplest ATCUN (amino terminal Cu(II) and Ni(II)-binding motif) peptide (NH-Gly-Gly-His-COOH, GGH) in the presence of ascorbate as an additive. In the following 4 decades, structural modifications of this complex were implemented, however, anticancer activity could not be significantly increased. This has led to neglecting the ATCUN motif and its Cu(II) complexes as potential chemotherapeutic agents.

CIME4R: Exploring iterative, AI-guided chemical reaction optimization campaigns in their parameter space.

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 for scientists to review or follow changes throughout the process. With the recent emergence of using artificial intelligence (AI) models to aid RO, another level of complexity has been added.

Functionalization of Ti64 via Direct Laser Interference Patterning and Its Influence on Wettability and Oxygen Bubble Nucleation.

The nucleation of bubbles on solid surfaces is an important phenomenon in nature and technological processes like electrolysis. During proton-exchange membrane electrolysis, the nucleation and separation of the electrically nonconductive oxygen in the anodic cycle plays a crucial role to minimize the overpotential it causes in the system. This increases the efficiency of the process, making renewable energy sources and the "power-to-gas" strategy more viable.

Gold(III) complexes with thiosemicarbazone ligands: insights into their cytotoxic effects on lung cancer cells.

Cancer continues to pose a global threat, underscoring the urgent need for more effective and safer treatment options. Gold-based compounds have recently emerged as promising candidates due to their diverse range of biological activities. In this study, three gold(III) complexes derived from thiosemicarbazone ligands have been synthesized, fully characterized, including their X-ray crystal structures.

Impact of N-heteroaromatic N-termini in Cu(II) ATCUN metallopeptides on their biorelevant redox activity.

Cu(II) complexes with ATCUN peptide ligands have been investigated for their ROS (reactive oxygen species) generation and oxidative DNA degradation abilities. The biological activity of most ATCUN complexes such as Cu-GGH (Gly-Gly-His) is, however, low. Tuning the redox chemistry by incorporation of N-heteroaromatics reinstates ROS production which leads to efficient DNA cleavage.

XSMILES: interactive visualization for molecules, SMILES and XAI attribution scores.

Background: 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 a predicted property. For this purpose, some XAI techniques calculate attribution scores associated with tokens of SMILES strings or with atoms of a molecule.

ChemInformatics Model Explorer (CIME): exploratory analysis of chemical model explanations.

The introduction of machine learning to small molecule research- an inherently multidisciplinary field in which chemists and data scientists combine their expertise and collaborate - has been vital to making screening processes more efficient. In recent years, numerous models that predict pharmacokinetic properties or bioactivity have been published, and these are used on a daily basis by chemists to make decisions and prioritize ideas. The emerging field of explainable artificial intelligence is opening up new possibilities for understanding the reasoning that underlies a model.

Incorporation of β-Alanine in Cu(II) ATCUN Peptide Complexes Increases ROS Levels, DNA Cleavage and Antiproliferative Activity.

Redox-active Cu(II) complexes are able to form reactive oxygen species (ROS) in the presence of oxygen and reducing agents. Recently, Faller et al. reported that ROS generation by Cu(II) ATCUN complexes is not as high as assumed for decades.

Collaborative Sense-Making in Genomic Research: The Role of Visualisation.

Genomic research emerges from collaborative work within and across different scientific disciplines. A diverse range of visualisation techniques has been employed to aid this research, yet relatively little is known as to how these techniques facilitate collaboration. We conducted a case study of collaborative research within a biomedical institute to learn more about the role visualisation plays in genomic mapping.

Forty Years after the Discovery of Its Nucleolytic Activity: [Cu(phen) ] Shows Unattended DNA Cleavage Activity upon Fluorination.

[Cu(phen) ] (phen=1,10-phenanthroline) is the first and still one of the most efficient artificial nucleases. In general, when the phen ligand is modified, the nucleolytic activity of its Cu complex is significantly reduced. This is most likely due to higher steric bulk of such ligands and thus lower affinity to DNA.

Visualizing metabolic network dynamics through time-series metabolomic data.

Background: New technologies have given rise to an abundance of -omics data, particularly metabolomic data. The scale of these data introduces new challenges for the interpretation and extraction of knowledge, requiring the development of innovative computational visualization methodologies. Here, we present GEM-Vis, an original method for the visualization of time-course metabolomic data within the context of metabolic network maps.

ClinVAP: a reporting strategy from variants to therapeutic options.

Motivation: Next-generation sequencing has become routine in oncology and opens up new avenues of therapies, particularly in personalized oncology setting. An increasing number of cases also implies a need for a more robust, automated and reproducible processing of long lists of variants for cancer diagnosis and therapy. While solutions for the large-scale analysis of somatic variants have been implemented, existing solutions often have issues with reproducibility, scalability and interoperability.

Flexible vs. rigid bis(2-benzimidazolyl) ligands in Cu(II) complexes: Impact on redox chemistry and oxidative DNA cleavage activity.

Cu(II) complexes of bis(2-benzimidazolyl) ligands connected by different linker moieties (disulfide, ethylene, ortho-phenylene) were applied in DNA cleavage reactions. Hydroxyl radicals and hydrogen peroxide were proven as reactive oxygen species (ROS) in a DNA quenching experiment. Thus, an oxidative DNA cleavage mechanism is suggested.

Unexpected features of the dark proteome.

We surveyed the "dark" proteome-that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, we found that 44-54% of the proteome in eukaryotes and viruses was dark, compared with only ∼14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions.

Integrated visual analysis of protein structures, sequences, and feature data.

Background: To understand the molecular mechanisms that give rise to a protein's function, biologists often need to (i) find and access all related atomic-resolution 3D structures, and (ii) map sequence-based features (e.g., domains, single-nucleotide polymorphisms, post-translational modifications) onto these structures.

Visualising intrinsic disorder and conformational variation in protein ensembles.

Intrinsically disordered regions (IDRs) in proteins are still not well understood, but are increasingly recognised as important in key biological functions, as well as in diseases. IDRs often confound experimental structure determination-however, they are present in many of the available 3D structures, where they exhibit a wide range of conformations, from ill-defined and highly flexible to well-defined upon binding to partner molecules, or upon post-translational modifications. Analysing such large conformational variations across ensembles of 3D structures can be complex and difficult; our goal in this paper is to improve this situation by augmenting traditional approaches (molecular graphics and principal components) with methods from human-computer interaction and information visualisation, especially parallel coordinates.

A visual analytics approach for models of heterogeneous cell populations.

In recent years, cell population models have become increasingly common. In contrast to classic single cell models, population models allow for the study of cell-to-cell variability, a crucial phenomenon in most populations of primary cells, cancer cells, and stem cells. Unfortunately, tools for in-depth analysis of population models are still missing.

An eQTL biological data visualization challenge and approaches from the visualization community.

In 2011, the IEEE VisWeek conferences inaugurated a symposium on Biological Data Visualization. Like other domain-oriented Vis symposia, this symposium's purpose was to explore the unique characteristics and requirements of visualization within the domain, and to enhance both the Visualization and Bio/Life-Sciences communities by pushing Biological data sets and domain understanding into the Visualization community, and well-informed Visualization solutions back to the Biological community. Amongst several other activities, the BioVis symposium created a data analysis and visualization contest.

iHAT: interactive hierarchical aggregation table for genetic association data.

In the search for single-nucleotide polymorphisms which influence the observable phenotype, genome wide association studies have become an important technique for the identification of associations between genotype and phenotype of a diverse set of sequence-based data. We present a methodology for the visual assessment of single-nucleotide polymorphisms using interactive hierarchical aggregation techniques combined with methods known from traditional sequence browsers and cluster heatmaps. Our tool, the interactive Hierarchical Aggregation Table (iHAT), facilitates the visualization of multiple sequence alignments, associated metadata, and hierarchical clusterings.

Evaluation of traditional, orthogonal, and radial tree diagrams by an eye tracking study.

Node-link diagrams are an effective and popular visualization approach for depicting hierarchical structures and for showing parent-child relationships. In this paper, we present the results of an eye tracking experiment investigating traditional, orthogonal, and radial node-link tree layouts as a piece of empirical basis for choosing between those layouts. Eye tracking was used to identify visual exploration behaviors of participants that were asked to solve a typical hierarchy exploration task by inspecting a static tree diagram: finding the least common ancestor of a given set of marked leaf nodes.

Continuous parallel coordinates.

Typical scientific data is represented on a grid with appropriate interpolation or approximation schemes,defined on a continuous domain. The visualization of such data in parallel coordinates may reveal patterns latently contained in the data and thus can improve the understanding of multidimensional relations. In this paper, we adopt the concept of continuous scatterplots for the visualization of spatially continuous input data to derive a density model for parallel coordinates.

Generation, annotation and analysis of ESTs from Trichoderma harzianum CECT 2413.

Background: The filamentous fungus Trichoderma harzianum is used as biological control agent of several plant-pathogenic fungi. In order to study the genome of this fungus, a functional genomics project called "TrichoEST" was developed to give insights into genes involved in biological control activities using an approach based on the generation of expressed sequence tags (ESTs).

Results: Eight different cDNA libraries from T.