Structure-based design is characterized by graphic-intense, interactive applications. Not surprisingly, up to day monolithic desktop applications dominate the software landscape in this area. Using modern JavaScript-based graphic plugins, several tasks in structure-based modeling can be transferred to the web. ProteinsPlus (http://proteins.plus) is an easy to use web service unifying access, assessment, and preprocessing of protein structures. Important processes like exploring ligands, predicting hydrogen positions and optimizing the hydrogen bond network, estimating electron density support, detecting binding pockets and estimating their druggability are fully integrated. Highly efficient database searches for active sites allow to quickly create structure ensembles, getting an overview of known bound ligands, active site mutations and conformational flexibility. A RESTful service enables the full integration into other web resources or even workflow systems like KNIME.<br/>As a second example, we present a cheminformatics web service named SMARTSview (http://smartsview.zbh.uni-hamburg.de). The design of SMARTS expressions usually applied for filtering compound collections remains a very technical procedure. To support it, we developed three software components: SMARTSview to visualize SMARTS expressions, SMARTSminer to create them from compound sets, and SMARTScompare to calculate the pattern similarity. All three of them are quite unique and available as a web service. With SMARTScompare, a method for searching chemical patterns in pattern collections like LINT or PAINS is made available for the first time.

ProteinsPlus and SMARTSviewer: Two web applications for the modeling and cheminformatics community

2019 Spring National Meeting

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