What is the STAP database?
STAP is a database of refined NMR structures that was obtained from the PDB. We presented a public database of 2,405 refined NMR solution structures in 2011. A simulated annealing protocol was employed to obtain refined structures with target potentials, including the newly developed STAP. The refined database was extensively analyzed using various quality indicators from several assessment programs to determine the nuclear Overhauser effect (NOE) completeness, Ramachandran appearance, chi1-chi2 rotamer normality, various parameters for protein stability and other indicators.
In 2016, we present an updated version of the previous database, STAP2.
The STAP2 database now includes,
(i) expanded dataset: 2,405 to 10,593 structures.
(ii) a newly develope refinement method: flat-bottom distance potential.
(iii) various structural analysis: 3D structure viewer, secondary structure scheme, and structural quality scores.
How to use STAP2 database?
Home; Search bar
Search refined structures in main page.
PDB ID or keyword search is available.
1. PDB id search example. (The minimum ID length is two.)
Figure 1. Search bar of Main page.
- (i) 3gb1 (PDB id)
- (ii) gb (part of PDB id)
2. Keyword search example.
Figure 2. Keyword search by fields
- (i) immunoglobulin (word)
- (ii) immun (part of word)
If you search structure by PDB id or keywords, the list page is shown.
Figure 3. List page.
In the list page, searched structures are shown by list form.
- General information
Users can identified the overall information of searched structures at a glance. Through this overall information, users can select target structures they want.
Searched structures basically include PDB id, Chain id, structure name, classification, compound, release date, experimental method, and number of amino acids.
- Database information
If users want to know other database information of listed structure, click the 'Database information' tab for identifying different type of information.
STAP2 database provides other database links such as PubMed, Taxonomy, CATH, SCOP, and Pfam, including Uniprot for understanding refined structures.
- Experimental informtaion
'Experimental information' tab shows experimental method information of NMR structure.
Figure 4. Result page.
Result page shows refined structure using STAP2 method with various analysis.
There are two tabs in the result page.
Refinement structure information is shown in 'Structure' tab and 'Properties' tab includes overall NMR structure information, molecular properties, and other database links.
1. Structure Tab
Refined structure name, domain name, PDB id, and chain id in the top of the result page. Red word indicates model number of NMR structures.
1) 3D structure viewer
3D strucure viewer shows before refined structure and after refined structure using Distance potential or NOE potential as 3D structure. Users can compare refined structure according to NMR structure model by clicking 'Model' button. 'All' button shows overlapped structure of before refined structure, dist refined structure, and NOE structure. Users can identify improved refined structure compared with original NMR structure. When users click 'Before', 'After(Dist)', and 'After(NOE)' buttons, each structure information are shown individually.
File download links are provided to save selected structure.
2) Control panel of refinement structure
Using 2D control panel, user can more understand part of refined structure results. Protein structure is presented as 2D form and different region between original structure and refined structures('Dist' and 'NOE') can identified at a glance. Blue indicates coil, Red indicated alpha helix, and Yellow indicated beta sheet. When users click a part of structure in control panel, selected position is highlighted at the 3D structure viewer.
The scores in the middle of result page is calculated to analyze refined structure. Users can compare after and before refined structure using each scores. 'Before' indicates before refined structure score lists, and 'After(Dist)' and 'After(NOE)' indicates after refined structures.
3) Comparison of refined structure quality by normalized structure validation scores
Two graphs below the score table show a degree of improvement of refined structure compared with original structure.
We normalized each protein like score results and presented percentage form. The good score is in inner circle. Shade region indecates upper 50%.
'X-ray space' graph shows score quality of current refined structure by X-ray structure standard. 'NMR space' graph shows score quality of current refined structure by NMR structure standard.
Red line means original structure, blue line means 'Dist' refined structure, and green line means 'NOE' refined structure.
2. Properties tab
Figure 5. Properties page.
Properties tab includes general information of target protein.
General information, molecular properties, and other database links are provided.