The era of big data is influencing the way how rational drug discovery and development bioactive molecules performed versatile tools are needed to assist in molecular design workflows. Scaffold Hunter a flexible visual analytics framework for analysis chemical compound combines techniques from several fields such as mining information visualization. allows analyzing high-dimensional an interactive fashion, combining intuitive visualizations with automated methods including clustering...

Abstract A common issue during drug design and development is the discovery of novel scaffolds for protein targets. On one hand chemical space purchasable compounds rather limited; on other artificially generated molecules suffer from a grave lack accessibility in practice. Therefore, we virtual library small which are synthesizable educts, called CH I PMUNK (CHemically feasible In silico Public Molecular UNiverse Knowledge base). Altogether, covers over 95 million encompasses regions that...

Abstract The growing interest in chemogenomics approaches over the last years has led to an increasing amount of data regarding chemical and corresponding biological activity space. resulting data, collected either in‐house or public databases, need be analyzed efficiently speed‐up increasingly difficult task drug discovery. Unfortunately, discovery new entities targets for known drugs (‘drug repurposing’) is not suitable a fully automated analysis simple drill down process. Visual...

Sequential agglomerative hierarchical non-overlapping (SAHN) clustering techniques belong to the classical methods applied heavily in many application domains, e.g., cheminformatics. Asymptotically optimal SAHN algorithms are known for arbitrary dissimilarity measures, but their quadratic time and space complexity even best case still limits applicability small data sets. We present a new pivot based heuristic algorithm exploiting properties of metric distance measures order obtain best-case...

Being able to quantify the similarity between two protein complexes is essential for numerous applications. Prominent examples are database searches known with a given query complex, comparison of output different complex prediction algorithms, or summarizing and clustering complexes, e.g., visualization. While corresponding problems have received much attention on single proteins families, question about how model compute has not yet been systematically studied. Because can be naturally...

We present a structural clustering algorithm for large-scale datasets of small labeled graphs, utilizing frequent subgraph sampling strategy. A set representatives provides an intuitive description each cluster, supports the process, and helps to interpret results. The projection-based nature approach allows us bypass dimensionality feature extraction problems that arise in context graph reduced pairwise distances or vectors. While achieving high quality (human) interpretable clusterings,...

Being able to quantify the similarity between two protein complexes is essential for numerous applications. Prominent examples are database searches known with a given query complex, comparison of output different complex prediction algorithms, or summarizing and clustering complexes, e.g., visualization. While corresponding problems have received much attention on single proteins families, question about how model compute has not yet been systematically studied. Because can be naturally...

The Cover Feature shows three chipmunks involved in the creation, analysis, and clustering of synthesizable virtual molecule library CHIPMUNK. Nearly 100 million compounds were generated with silico reactions on accessible building blocks, their descriptor profile was analysed. clustered together molecules from other public libraries order to relate it known chemical space divide huge into manageable subsets. It serves as an idea generator covers beyond rule five protein–protein well...

The growing interest in chemogenomics approaches over the last years has led to a vast amount of data regarding chemical and corresponding biological activity space. discovery new entities is not suitable fully automated analysis, but can greatly benefit from tools that allow exploring this We present version Scaffold Hunter [1,2], highly interactive tool fosters systematic visual exploration compound bioactivity data. software supports integration various sources provides several...