Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace

Abstract

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.

Keywords: in silico drug design; chemical biology; virtual screening.

Figure 1

Virtual screening online. Several research laboratories worldwide provide online virtual screening services. In the present survey, the identified main countries offering online virtual screening services (active URLs in February 2020) are (by alphabetic order): Austria, Australia, Brazil, Canada, China, Czech Republic, Denmark, France, Germany, India, Israel, Italy, Japan, Poland, Republic of Ecuador, Republic of Korea, Saudi Arabia, Spain, Switzerland, The Netherlands, Taïwan, Turkey, the UK and the USA. The map chart was created with Mapchart.net. The main LBVS methods are 2D similarity search, pharmacophores, QSAR models and shape/field alignments while for SBVS, the approaches involve docking, scoring and rescoring with various methods including consensus scoring, or different flavors of free energy calculations.