Abstract
In silico assessment of protein receptor interactions with small ligands is now part of the standard pipeline for drug discovery, and numerous tools and protocols have been developed for this purpose. With the SeamDock web server, we propose a new approach to facilitate access to small molecule docking for nonspecialists, including students. The SeamDock online service integrates different docking tools in a common framework that allows ligand global and/or local docking and a hierarchical approach combining the two for easy interaction site identification. This service does not require advanced computer knowledge, and it works without the installation of any programs with the exception of a common web browser. The use of the Seamless framework linking the RPBS calculation server to the user’s browser allows the user to navigate smoothly and interactively on the SeamDock web page. A major effort has been put into the 3D visualization of ligand, receptor, and docking poses and their interactions with the receptor. The advanced visualization features combined with the seamless library allow a user to share with an unlimited number of collaborators, a docking session, and its full visualization states. As a result, SeamDock can be seen as a free, simple, didactic, evolving online docking resource best suited for education and training.
Highlights
Molecular docking is a computational tool that attempts to predict the structure of interaction between a protein and a molecule
Users can proceed to a molecular docking without extensive computing or biophysics knowledge
SeamDock’s ease of use combined with a complete 3D visualization in a SeamDock collaborative mode makes it a perfect tool for nonspecialists outside of the molecular modeling community. It can be used in a collaborative mode with partners all around the world or in a classroom focused on docking methods or receptor–ligand interactions, while ignoring software installation and Unix command lines
Summary
Molecular docking is a computational tool that attempts to predict the structure of interaction between a protein and a molecule. Docking programs are a combination of a search algorithm and a scoring function. The scoring function purpose is the prediction of the binding affinity in order to evaluate how well the ligands bind to the protein. In parallel, docking developments have been proposed to address more specific questions such as the search for protein–protein interaction (PPI) inhibitors (Ran and Gestwicki, 2018), allosteric drugs (Wagner et al, 2020), or fragment-based approaches (Shan et al, 2020). Molecular docking protocols are widely used to develop new drugs and are an important part of the drug discovery pipeline at pharmaceutical companies (Muegge et al, 2017). Include in their pipeline, the use of docking software such
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