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To understand biological processes, interpreting genomic data is crucial. Protein structures aid in this interpretation by providing functional context for genomic coding regions. Mapping genes to proteins is simple, but inconsistencies in data formats can make it a tedious and error-prone process. Over the last 20 years, more than 20 different tools or databases have been developed to automatically map annotated positions and variants to protein structures. However, most of these methods are web-based tools, which is not ideal for dealing with large-scale genomic data. To address this, we introduce 3Dmapper, a standalone Python/R command line tool that systematically maps annotated protein positions or variants to protein structures.
3Dmapper is a command-line tool that integrates structural and genomic data to identify and visualize variants on protein structures. The pipeline consists of four steps, including the generation of a structural database, variant annotation and splitting, variant mapping to protein structures, and visualization with ChimeraX. 3Dmapper enables users to identify the functional effects of variants, their locations in relation to the protein structure, and ultimately, their potential involvement in disease. The pipeline is customizable and can be used with any protein structure, facilitating the identification of variants in proteins of interest.
