"Spruce – High-Throughput Curation and Preparation of Crystal Structures for Structure-Based Design" was presented by Jesper Soerensen, Senior Scientific Software Developer at OpenEye, on Wednesday, December 18, 2019 at 12pm EDT / 9am PDT (US).
Structure-based drug design requires careful preparation of experimental structures for downstream modeling applications. In this work we will introduce SPRUCE, an application for biomolecular structure preparation and model assessment, which is backed by the new Spruce Toolkit. Here, we will highlight SPRUCE's structure preparation workflow, including hydrogen network optimization with ligand tautomer searching, and model quality assessment using the Iridium classification. Additionally, we will present the results of a cross-docking experiment using POSIT on hundreds of receptors, as well as the results of subsequent short trajectory MD run for each pose. The prep, docking and MD simulations were all performed in the cloud using Orion.