Type 'PDB ID' or 'Keyword' of structure, and click the 'Search' button.
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About
What's new?
How to use STAP2?
What is the STAP2?
  • STAP2 is database of refined NMR structures. STAP2 refined the almost all NMR structures deposited in PDB (10,583) using statistical torsion angle potential and structurally- or experimentally- derived distance potential. The refined structures have more significantly improved structural quality than their initial NMR structure. The structural quality of initial and refined NMR structure is provided by various structural analysis. We believe that the STAP2 is useful to study of protein structure by providing refined NMR structures with high structural quality.
Expanded datasets New method
  • Flat-bottom distance potential that is newly developed NOE-like distance potential generated from initial NMR structure.
  • More detailed information
Various structural analysis
  • 3D structure view, secondary structure scheme, tabular (score table) and graphical scores (radar charts).
  • More detailed information
PDB ID Search
  • Please select the 'PDB ID' in field selection menu and enter the PDB ID of the NMR structure into search box.
  • PDB ID should contain two or more characters (ex. '3g' or '3gb1' ).
Keyword Search
  • If you do not have a PDB ID, you can find refined structure through a several keyword search.
  • For example, if you select 'Classification' in field selection menu and enter 'membrane' into search box, you can see the list of membrane associated structures.
References
  1. First version of STAP : Yang, J.S., Kim, J.H., Oh, S., Han, G., Lee, S. and Lee, J. (2012) STAP Refinement of the NMR database: a database of 2405 refined solution NMR structures. Nucleic acids research, 40, D525-530.
  2. Method paper of STAP : Kim, T.R., Yang, J.S., Shin, S. and Lee, J. (2013) Statistical torsion angle potential energy functions for protein structure modeling: a bicubic interpolation approach. Proteins, 81, 1156-1165.
  3. Method paper of flat-bottom distance potential : Ryu, H., Kim, T.R., Ahn, S., Ji, S. and Lee, J. (2014) Protein NMR structures refined without NOE data. PloS one, 9, e108888
  4. Web server for NMR structure refinement : Ryu, H., Lim, GT., Sung, BH. and Lee, J. (2016) NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores. Bioinformatics, 32.4, 611-613