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DB3:

A database of protein-protein complexes consisting of 1879 co-crystallized interacting native structures (each containing two chains) with resolution better than 2 Å, and no missing backbone atoms; The database was assembled using the ‘Build Database' option from Dockground [1] and used before in protein-protein docking scoring [2], structure validation of PPI complexes [3] and in probing the role salt-bridges in protein-protein interfaces [4]. Hydrogen atoms were geometrically fixed to all structures using REDUCE [5], version. 2 [6].

References:

1. Protein models: the grand challenge of protein docking. Anishchenko I. et al. Proteins Struct. Funct. Bioinforma, 2014, 82, 278–287.

2. Finding correct protein-protein docking models using ProQDock. Sankar Basu, Bjorn Wallner* Bioinformatics. 2016, 32 (12): i262-i270. doi: 10.1093/bioinformatics/btw257

3. SARAMAint: The Complementarity Plot for Protein-Protein Interface Sankar Basu, Dhananjay Bhattacharyya, and Bjorn Wallner* Journal of Bioinformatics and Intelegent Controll, 2014, 3:309-314.

4. Salt-bridge Networks within Globular and Disordered Proteins - Characterizing Trends for Designable Interactions. Sankar Basu* and Debasish Mukharjee Journal of Molecular Modeling, (2017) 23:206 DOI: 10.1007/s00894-017-3376-y

5. Asparagine and glutamine: using hydrogen atom contacts in the choice of sidechain amide orientation, Word, et al., 1999, J. Mol. Biol. 285, 1735-1747.

6. http://kinemage.biochem.duke.edu/downloads/software/reduce/reduce.2.21.mod040509dcr.linux.RH9