DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins

Area of Science:

• Protein structure and stability
• Bioinformatics and computational biology
• Structural bioinformatics

Background:

• Disulphide bonds are crucial for protein stability, particularly in small, disulphide-rich proteins.
• Their positional conservation can indicate protein family and functional relationships.
• A comprehensive, publicly accessible database for disulphide crosslinks has been absent.

Purpose of the Study:

• To present DSDBASE2.0, an updated and expanded database of native and modeled disulphide bonds.
• To provide enhanced computational tools for analyzing proteins with disulphide crosslinks.
• To serve as a central, open-access repository for disulphide bond information.

Main Methods:

• Manual curation and annotation of native and modeled disulphides.
• Development of the Modelling of Disulphides in Proteins (MODIP) algorithm for disulphide bond modeling.
• Integration of PDB data up to January 2021, including 153,944 entries.
• Implementation of user-friendly search functions and tools like RANMOD for 3D model generation.

Main Results:

• DSDBASE2.0 contains 216,096 native and 20,153,850 modeled disulphide bond segments.
• The database offers annotations for function (GO) and subcellular localization.
• Computational tools facilitate the recognition of compatible polypeptide segments and modeling of disulphide-rich proteins.

Conclusions:

• DSDBASE2.0 is the largest open-access repository for protein disulphide bonds.
• The database and associated tools significantly advance research on protein structure, stability, and function.
• It provides a valuable resource for identifying and modeling disulphide crosslinks in proteins.