SwissSimilarity: A Web Tool for Low to Ultra High Throughput Ligand-Based Virtual Screening

Abstract

SwissSimilarity is a new web tool for rapid ligand-based virtual screening of small to unprecedented ultralarge libraries of small molecules. Screenable compounds include drugs, bioactive and commercial molecules, as well as 205 million of virtual compounds readily synthesizable from commercially available synthetic reagents. Predictions can be carried out on-the-fly using six different screening approaches, including 2D molecular fingerprints as well as superpositional and fast nonsuperpositional 3D similarity methodologies. SwissSimilarity is part of a large initiative of the SIB Swiss Institute of Bioinformatics to provide online tools for computer-aided drug design, such as SwissDock, SwissBioisostere or SwissTargetPrediction with which it can interoperate, and is linked to other well-established online tools and databases. User interface and backend have been designed for simplicity and ease of use, to provide proficient virtual screening capabilities to specialists and nonexperts in the field. SwissSimilarity is accessible free of charge or login at http://www.swisssimilarity.ch .

SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules

“…One-click interoperability gives access to various CADD tools developed by the Molecular Modeling Group of the SIB Swiss Institute of Bioinformatics, e.g. ligand-based virtual screening (SwissSimilarity18), biotarget prediction (SwissTargetPrediction19), molecular docking (SwissDock20), bioisosteric design (SwissBioisostere21), or molecular mechanics (SwissParam22). …”

Bioinformatics and Drug Discovery

“…Such tools include SWISS-MODEL [213] and TASSER [214] and its derivatives. Once the structure is refined, one can use UCSF Chimera [215] or PyMOL (The PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC) to visualize the structure and use automated screening software such as SwissSimilarity [216] to identify potential drug candidate that can interact with the protein of interest. Such screening approach is greatly enhanced by metabolic and ligand databases such ChEMBL [217] and SuperSite [218].…”

“…Many software packages are powerful and free, and supported by well-known institutions. These include databases such as ChEMBL [217] and SwissSidechain [255], software tools such as UCSF Chimera [215] which is not only a 3D visualization tool but also a platform for software developers interested in structural biology, SwissSimilarity for virtual screening [216], SwissBioisostere for ligand design [220], SwissTargetPrediction [226], SwissSideChain to facilitate experiments that expand the protein repertoire by introducing non-natural amino acids, and SwissDock [219] for docking drug candidates (small molecules) on proteins. Although some software are commercial, e.g.…”

eSHAFTS: Integrated and graphical drug design software based on 3D molecular similarity

“…These software can be divided into three categories, which are based on three‐dimensional (3D) similarity, pharmacophore matching, and molecular docking separately. The virtual screening software based on 3D similarity include LiSCA, SwissSimilarity, VSViewer3D, ChemMapper, and so on. The virtual screening software based on pharmacophore matching include Phase, Catalyst, LigandScout, MOE, and so on.…”