From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library

Abstract Nowadays, computational approaches are an integral part of life science research. Problems related to interpretation of experimental results, data analysis, or visualization tasks highly benefit from the achievements of the digital era. Simulation methods facilitate predictions of physicochemical properties and can assist in understanding macromolecular phenomena. Here, we will give an overview of the methods developed in our group that aim at supporting researchers from all life science areas. Based on state-of-the-art approaches from structural bioinformaticsand cheminformatics, we provide software covering a wide range of research questions. Our all-in-one web service platform Proteins Plus ( http://proteins.plus ) offers solutions for pocket and druggabilityprediction, hydrogen placement, structure quality assessment, ensemble generation, protein–protein interaction classification, and 2D- interaction visualization. Additionally, we provide a software package that contains tools targeting cheminformaticsproblems like file formatconversion, molecule data set processing, SMARTS editing, fragment space enumeration, and ligand-based virtual screening. Furthermore, it also includes structural bioinformaticssolutions for inverse screening, binding site alignment, and searching interaction patterns across structure libraries. The software package is available at http://software.zbh.uni-hamburg.de .