Highlights•Drug discovery data and data from other sources are different in quantity and
characteristics.•This article underlines the difference of data from different domains.•In order …

Molecular fingerprints have been used for a long time now in drug discovery and virtual
screening. Their ease of use (requiring little to no configuration) and the speed at which …

Small organic molecules are often flexible, ie, they can adopt a variety of low-energy
conformations in solution that exist in equilibrium with each other. Two main search …

Despite their enormous potential, machine learning methods have only found limited
application in predicting reaction outcomes, because current models are often highly …

Machine learning algorithms are generally developed in computer science or adjacent
disciplines and find their way into chemical modeling by a process of diffusion. Though …

Successful deep learning critically depends on the representation of the learned objects.
Recent state-of-the-art pharmaceutical deep learning models successfully exploit graph …

Motivation: Most bioactive molecules perform their action by interacting with proteins or other
macromolecules. However, for a significant fraction of them, the primary target remains …

Autodock Vina is a very popular, and highly cited, open source docking program. Here we
present a scoring function which we call Vinardo (Vina RaDii Optimized). Vinardo is based …

Highlights•Providing concepts and generation processes of chemical fingerprints.•
Comparing the algorithms and characteristics among different types of fingerprints.• …

Molecular similarity is a key concept in drug discovery. It is based on the assumption that
structurally similar molecules frequently have similar properties. Assessment of similarity …