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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: 1OLG
Structure validation scores

nmr_space

Description
Our cells face many dangers, including chemicals, viruses, and ionizing radiation. If cells are damaged in sensitive places by these attackers, the effects can be disastrous. For instance, if key regulatory elements are damaged, the normal controls on cell growth may be blocked and the cell will rapidly multiply and grow into a tumor. p53 tumor suppressor is one of our defenses against this type of damage. p53 tumor suppressor is normally found at low levels, but when DNA damage is sensed, p53 levels rise and initiate protective measures. p53 binds to many regulatory sites in the genome and begins production of proteins that halt cell division until the damage is repaired. Or, if the damage is too severe, p53 initiates the process of programmed cell death, or apoptosis, which directs the cell to commit suicide, permanently removing the damage.
(http://pdb101.rcsb.org/motm/31)

• 1OLG 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