SSSDb

SSSDb provides coarse-grained representations of biomolecular structures, specifically focusing on CATH protein domains, to reduce computational loads in structural analyses such as database docking studies and simulations.

Key Features:

• Coarse-grained structural representations: The database offers surface and a spectrum of deterministically sampled shape representations at varied fineness for biomolecular structures.
• CATH domain coverage: Phase I contains 988,124 coarse-grained structures of 31,885 CATH protein domains.
• Multiple access options: Data retrieval is supported through CATH ID based queries, precompiled data clusters, entire database download as a single zip file, and customizable automated downloads using programming scripts.

Scientific Applications:

• Database docking studies: The reduced representations enable whole database docking studies that would otherwise be computationally prohibitive.
• Molecular simulations: Coarse-grained models facilitate microsecond simulations by decreasing computational requirements.
• Pairwise comparisons: The database supports pairwise comparisons of entire molecular repositories through simplified structural representations.

Methodology:

SSSDb generates deterministically sampled surface and shape representations of biomolecular structures at varied fineness levels.