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About

What is the STAP2?
STAP2 refined the almost all NMR structures deposited in PDB (10,608) 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.
(10,608 structures, as of May 2018)
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: 1IBN
Structure validation scores

nmr_space

Description
Influenza virus is a dangerous enemy. Normally, the immune system fights off infections, eradicating the viruses and causing a few days of miserable flu symptoms. Yearly flu vaccines prime our immune system, making it ready to fight the most common strains of influenza virus. But once every couple of decades, a new strain of influenza appears that is far more pathogenic, allowing it to spread rapidly. This happened at the end of World War I, and the resultant pandemic killed over 20 million people, more than twice the number of people that were killed in the war.
(http://pdb101.rcsb.org/motm/76)

• 1IBN 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