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About

What is the STAP2?
STAP2 refined the almost all NMR structures deposited in PDB (10,593) 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.
How to link?
• http://psb.kobic.re.kr/stap2/index.cgi?PDB ID

What's new?

Expanded datasets
• Most of NMR structures in PDB.
(10,593 structures, as of June 2015)
More detailed information
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

How to STAP2?

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.

Biologically interesting example of refined structure

PDB ID: 1C9F
Structure validation scores

nmr_space

Description
Billions of cells in your body will die in the next hour. This is entirely normal--the human body continually renews itself, removing obsolete or damaged cells and replacing them with healthy new ones. However, your body must do this carefully. If cells are damaged, like when you cut yourself, they may swell and burst, contaminating the surrounding area. The body responds harshly to this type of cell death, inflaming the area by rushing in blood cells to clean up the mess. To avoid this messy problem, your cells are boobytrapped with a method to die cleanly and quickly on demand. When given the signal, the cell will disassemble its own internal structure and fragment itself into small, tidy pieces that are readily consumed by neighboring cells. This process of controlled, antiseptic death is called apoptosis.
(http://pdb101.rcsb.org/motm/56)

• 1C9F refinement result

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