PRISM: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact

Motivation: Post-translational modifications (PTMs) play very important roles in various cell signalling pathways and biological process. Due to PTMs9 extremely important roles, many major PTMs have been thoroughly studied, while the functional and mechanical characterization of major PTMs is well-documented in several databases. However, currently available databases only focus on protein sequences, while the real 3D structures of PTMs have been largely ignored. Therefore, studies of PTMs 3D structural signatures have been severely limited by the deficiency of the data. Results: Here, we developed PRISM, a novel publicly available and free 3D structure-based database for PTMs. PRISM provides comprehensive and interactive online knowledge focused on 3D structural information of PTM proteins. The first version of PRISM encompasses 17,145 non-redundant modification sites on 3,919 related protein 3D structure entries pertaining to 37 different types of PTMs. Our entry web page organizes in a comprehensive manner detailed PTM annotation on the 3D structure and biological information in terms of mutations affecting PTMs information, secondary structural features and residue accessibility features of PTM sites, domain context information, predicted disordered regions and sequence alignments. In addition, high-definition JavaScript packages are employed to enhance information visualization in PRISM. PRISM equips a variety of interactive and customizable search options and data browsing functions; these capabilities allow users to access data via keyword, ID, and advanced options combination search in an efficient and user-friendly way. A download page is also provided to enable users to download the SQL file, computational structural features, and PTM sites9 data. We anticipate PRISM will swiftly become an invaluable online resource, assisting both biologists and bioinformaticians to conduct experiments and develop applications supporting discovery efforts in the sequence-structural-functional relationship of PTMs and providing important insight into mutations and PTM sites interaction mechanisms.