Opening the door to PDB data with OneDep
Cell Press’ CrossTalk blog interviewed Biocurator Chenghua Shao on his recent publication examining the impact of the wwPDB’s OneDep system for biocuration, and validation on PDB data quality:
Multivariate Analyses of Quality Metrics for Crystal Structures in the Protein Data Bank Archive. Structure (2017) C. Shao, H. Yang, J. D. Westbrook, J. Y. Young, C. Zardecki, S. K. Burley. http://dx.doi.org/10.1016/j.str.2017.01.013
These analyses show how structure quality improved from the wwPDB OneDep system versus legacy PDB systems. There was however, little improvement in ligand quality from the OneDep system versus legacy systems. As Chenghua notes in his interview, the wwPDB is working to change this by incorporating recommendations developed at the 2015 Ligand Validation Workshop within the system.
A paper describing the OneDep system was also recently published in Structure:
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the Protein Data Bank (PDB) Archive. Structure (2017) J. Young, J. D. Westbrook, Z. Feng, R. Sala, E. Peisach, T. J. Oldfield, S. Sen, A. Gutmanas, D. R. Armstrong, J. M. Berrisford, L. Chen, M. Chen, L. Di Costanzo, D. Dimitropoulos, G. Gao, S. Ghosh, S. Gore, V. Guranovic, P. M. S. Hendrickx, B. P. Hudson, R. Igarashi, Y. Ikegawa, N. Kobayashi, C. L. Lawson, Y. Liang, S. Mading, L. Mak, M. S. Mir, A. Mukhopadhyay, A. Patwardhan, I. Persikova, L. Rinaldi, E. Sanz-Garcia, M. R. Sekharan, C. Shao, G. J. Swaminathan, L. Tan, E. L. Ulrich, G. Van Ginkel, R. Yamashita, H. Yang, M. A. Zhuravleva, M. Quesada, G. J. Kleywegt, H. M. Berman, J. L. Markley, H. Nakamura, S. Velankar, S. K. Burley. http://dx.doi.org/10.1016/j.str.2017.01.004.
CrossTalk also described the role of Biocuration and OneDep in another article OneDep is a step in the right direction.