DSDBASE

DSDBASE catalogs disulphide bonds in proteins, providing curated native and modeled disulphide segments and associated annotations to support structural and functional analysis.

Key Features:

• Manual curation and annotation: Curated entries describe native and modelled disulphide bonds with functional annotations including Gene Ontology (GO) terms and subcellular localization.
• Native and modelled disulphide segments: Dataset derived from 153,944 PDB entries (Protein Data Bank, January 2021) comprising 216,096 native and 20,153,850 modelled disulphide bond segments.
• MODIP modelling: Uses the Modelling of Disulphides in Proteins (MODIP) algorithm to predict stereochemically possible disulphide crosslinks and expand the loop database for template recognition.
• RANMOD conformational sampling: Employs the RANMOD algorithm to generate and examine random but stereochemically allowed backbone conformations of polypeptides for three-dimensional modelling of disulphide-rich small proteins.
• Structural constraints information: Records the influence of disulphide bonds on backbone conformations, thermal stability, and protein conformational states.

Scientific Applications:

• Protein structural analysis: Enables analysis of how disulphide bonds stabilize protein structures and constrain backbone conformations.
• Modeling disulphide-rich proteins: Supports three-dimensional modelling of small proteins containing multiple disulphide crosslinks using RANMOD and MODIP-derived templates.
• Template recognition for loop modelling: Facilitates identification of compatible polypeptide segments as templates for immediate structural modelling via the expanded loop database.
• Functional and evolutionary inference: Aids study of protein family associations and functional linkages through positional conservation of disulphide crosslinks.

Methodology:

Modelled disulphide segments were generated from PDB entries (January 2021) and predicted using the MODIP algorithm for stereochemically possible crosslinks; RANMOD generates and examines random stereochemically allowed backbone conformations of polypeptides.