ModelArchive
From Proteopedia
ModelArchive is the archive for theoretical macromolecular structure models that are not based on experimental data (not empirical). Such models were removed from the wwPDB in 2006[1]. ModelArchive complements the wwPDB archive of empirical models, and the PDB-Dev archive for integrative structures that combine non-empirical and empirical models.[2]
Purpose
"The main purpose of a deposited model is to supplement a manuscript for which the model was generated and to make the model accessible for the interested reader. The secondary purpose is to make all deposited models findable, accessible, interoperable and reusable (FAIR) for interested researchers. As a result, ModelArchive provides a unique stable accession code (DOI) for each deposited model, which can be directly referenced in the corresponding manuscripts."[3]
Contents
"Any type of macromolecular structure which would otherwise be suitable for the PDB but whose coordinates are not based on experimental data can be deposited in ModelArchive." "The modelling methods can be pure in silico predictions as found in de novo models or based on experimental structures such as homology models or modified structures including docked ligands, modelled variants, post-translational modifications (e.g. glycosylated structures), etc."[3]
In August, 2024, ModelArchive contains about 2,300 models, listed most recent first. There are about 1,000 models deposited beginning in 2013. Prior to 2013, about 1,300 models are "legacy models", non-empirical models that were originally deposited in the wwPDB between 1978 and 2006, and subsequently removed.
References
- ↑ Berman HM, Burley SK, Chiu W, Sali A, Adzhubei A, Bourne PE, Bryant SH, Dunbrack RL Jr, Fidelis K, Frank J, Godzik A, Henrick K, Joachimiak A, Heymann B, Jones D, Markley JL, Moult J, Montelione GT, Orengo C, Rossmann MG, Rost B, Saibil H, Schwede T, Standley DM, Westbrook JD. Outcome of a workshop on archiving structural models of biological macromolecules. Structure. 2006 Aug;14(8):1211-7. PMID:16955948 doi:10.1016/j.str.2006.06.005
- ↑ This paragraph is paraphrased from the ModelArchive.Org website.
- ↑ 3.0 3.1 Quoted from ModelArchive Help.
