The interplay between life sciences and advancing technology drives a continuous cycle of chemical data growth; these data are most often stored in open or partially open databases. In parallel, many different types of algorithms are being developed to manipulate these chemical objects and associated bioactivity data. Virtual screening methods are among the most popular computational approaches in pharmaceutical research. Today, user-friendly web-based tools are available to help scientists perform virtual screening experiments. This article provides an overview of internet resources enabling and supporting chemical biology and early drug discovery with a main emphasis on web servers dedicated to virtual ligand screening and small-molecule docking. This survey first introduces some key concepts and then presents recent and easily accessible virtual screening and related target-fishing tools as well as briefly discusses case studies enabled by some of these web services. Notwithstanding further improvements, already available web-based tools not only contribute to the design of bioactive molecules and assist drug repositioning but also help to generate new ideas and explore different hypotheses in a timely fashion while contributing to teaching in the field of drug development.

SUMMARY: Several web-based tools predict the putative targets of a small molecule query compound by similarity to molecules with known bioactivity data using molecular fingerprints. In numerous situations, it would however be valuable to be able to run such computations on a local computer. We present FastTargetPred, a new program for the prediction of protein targets for small molecule queries. Structural similarity computations rely on a large collection of confirmed protein-ligand activities extracted from the curated ChEMBL 25 database. The program allows to annotate an input chemical library of ∼100k compounds within a few hours on a simple personal computer. AVAILABILITY AND IMPLEMENTATION: FastTargetPred is written in Python 3 (≥3.7) and C languages. Python code depends only on the Python Standard Library. The program can be run on Linux, MacOS and Windows operating systems. Pre-compiled versions are available at https://github.com/ludovicchaput/FastTargetPred. FastTargetPred is licensed under the GNU GPLv3. The program calls some scripts from the free chemistry toolkit MayaChemTools. CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.