RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB

Motivation Membrane proteins are encoded by approximately one fifth of human genes but account for more than half of all US FDA approved drug targets. Thanks to new technological advances, the number of membrane proteins archived in the PDB is growing rapidly. However, automatic identification of membrane proteins or inference of membrane location is not a trivial task. Results We present recent improvements to the RCSB Protein Data Bank web portal (RCSB PDB, rcsb.org) that provide a wealth of new membrane protein annotations integrated from four external resources: OPM, PDBTM, MemProtMD and mpstruc. We have substantially enhanced the presentation of data on membrane proteins. The number of membrane proteins with annotations available on rcsb.org was increased by similar to 80%. Users can search for these annotations, explore corresponding tree hierarchies, display membrane segments at the 1D amino acid sequence level, and visualize the predicted location of the membrane layer in 3D. Availability and implementation Annotations, search, tree data and visualization are available at our rcsb.org web portal. Membrane visualization is supported by the open-source Mol* viewer (molstar.org and github.com/molstar/molstar). Supplementary information are available at Bioinformatics online.

Automated summary

Membrane proteins, encoded by a significant portion of human genes, account for a majority of FDA-approved drug targets. The RCSB Protein Data Bank web portal has made recent improvements by integrating a wealth of new membrane protein annotations from external resources. These enhancements greatly enhance the presentation of membrane protein data and provide users with tools for searching and visualizing these proteins.