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 …

SwissTargetPrediction is a web tool, on-line since 2014, that aims to predict the most
probable protein targets of small molecules. Predictions are based on the similarity principle …

Bioactive small molecules, such as drugs or metabolites, bind to proteins or other macro-
molecular targets to modulate their activity, which in turn results in the observed phenotypic …

Reports of successful applications of machine learning (ML) methods in structure-based
virtual screening (SBVS) are increasing. ML methods such as convolutional neural networks …

In this work, we propose a deep learning approach to improve docking-based virtual
screening. The deep neural network that is introduced, DeepVS, uses the output of a …

SwissSimilarity is a new web tool for rapid ligand-based virtual screening of small to
unprecedented ultralarge libraries of small molecules. Screenable compounds include …

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 …

This work introduces a number of algebraic topology approaches, including multi-
component persistent homology, multi-level persistent homology, and electrostatic …

One of the main challenges of structure-based virtual screening (SBVS) is the incorporation
of the receptor's flexibility, as its explicit representation in every docking run implies a high …