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ChemBioServer 2.0: An Advanced Web Server for Filtering, Clustering and Networking of Chemical Compounds Facilitating Both Drug Discovery and Repurposing

submitted on 05.07.2019, 20:42 and posted on 08.07.2019, 13:52 by Evangelos Karatzas, Juan Eiros Zamora, Emmanouil Athanasiadis, Dimitris Dellis, Zoe Cournia, George Spyrou

ChemBioServer 2.0 is the advanced sequel of a web-server for filtering, clustering and networking of chemical compound libraries facilitating both drug discovery and repurposing. It provides researchers the ability to (i) browse and visualize compounds along with their physicochemical and toxicity properties, (ii) perform property-based filtering of chemical compounds, (iii) explore compound libraries for lead optimization based on perfect match substructure search, (iv) re-rank virtual screening results to achieve selectivity for a protein of interest against different protein members of the same family, selecting only those compounds that score high for the protein of interest, (v) perform clustering among the compounds based on their physicochemical properties providing representative compounds for each cluster, (vi) construct and visualize a structural similarity network of compounds providing a set of network analysis metrics, (vii) combine a given set of compounds with a reference set of compounds into a single structural similarity network providing the opportunity to infer drug repurposing due to transitivity, (viii) remove compounds from a network based on their similarity with unwanted substances (e.g. failed drugs) and (ix) build custom compound mining pipelines. The updated web server is available in the URL:


European Commission Research Executive Agency (REA) Grant BIORISE (Num. 669026)

European Union’s Horizon 2020 Framework Programme for Research and Innovation under Grant Agreement No. 785907 (Human Brain Project SGA2)


Email Address of Submitting Author


The Cyprus Institute of Neurology and Genetics



ORCID For Submitting Author


Declaration of Conflict of Interest

No conflict of interest