Sampled Surface and Shape DataBase (SSSDb): A database of deterministically sampled surface and a spectrum of shape representations of biomolecular structures
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Computational tools and techniques have come a long way in analyzing biomolecular structures. However, there are still limitations in how far we can exhaustively utilize the structural information of molecules in applications like whole database docking studies, achieving microsecond simulations , performing pairwise comparisions of entire molecular repositories. Coarse Grained models biomolecular structures have potential applications in many such methodologies as they help reduce the computational loads. SSSDb is a resource of such reduced representations of biomole-cular structures and provides surface and a spectrum of deterministically sampled shapes at varied fineness. Phase I of SSSDb provides 9,88,124 (? 1 million) coarse grained structures of 31,885 CATH protein domains. To cater the different possible needs of users the database is also provisioned to be accessible through four different options: (1) CATH ID based queires, (2) precompiled data clusters, (3) entire database download as single zip file and (4) customizable and automated downloads using programming script. In near future, SSSDb will be expanded to include all the biomolecular structures of Protein, DNA, RNA and their complexes. The entire database is available freely and openly for both academic and non-academic purposes