Statistics Summary Report for NYCOMPS Center
Last updated: Mar 11 2010
Target Status Statistics
Total number of targets deposited by NYCOMPS to TargetDB: 9343
View NYCOMPS Target ListTable 1: Status Statistics for NYCOMPS
| Status | Total Number of Targets | (%) Relative to "Cloned" Targets | (%) Relative to "Expressed" Targets | (%) Relative to "Purified" Targets | (%) Relative to "Crystallized" Targets |
| Cloned | 8630 | 100.0 | - | - | - |
| Expressed | 2669 | 30.9 | 100.0 | - | - |
| Soluble | 277 | 3.2 | 10.4 | - | - |
| Purified | 603 | 7.0 | 22.6 | 100.0 | - |
| Crystallized | 3 | 0.0 | 0.1 | 0.5 | 100.0 |
| Diffraction-quality Crystals | 5 | 0.1 | 0.2 | 0.8 | 166.7 |
| Diffraction | 4 | 0.0 | 0.1 | 0.7 | 133.3 |
| NMR Assigned | 0 | 0.0 | 0.0 | 0.0 | - |
| HSQC | 0 | 0.0 | 0.0 | 0.0 | - |
| Crystal Structure | 2 | 0.0 | 0.1 | 0.3 | 66.7 |
| NMR Structure | 0 | 0.0 | 0.0 | 0.0 | - |
| In PDB1 | 4 | 0.0 | 0.1 | 0.7 | 133 |
| Work Stopped | 6861 | - | - | - | - |
| Test Target | 0 | - | - | - | - |
| Other | 495 | - | - | - | - |
Table 2: Status Statistics for NYCOMPS by Organism
These statistics are derived from mapping of target sequences to GenBank using
>=98% sequence identity cut off
| Organism | Total Number1 | Work Stopped | Cloned | Expressed | Purified | Crystallized | Crystal Structure | NMR Structure | In PDB2 |
| Viruses | 6 | 3 | 6 | 3 | 2 | 0 | 0 | 0 | 0 |
| Archaea | 916 | 733 | 788 | 181 | 30 | 1 | 0 | 0 | 1 |
| Bacteria | 8338 | 6123 | 7753 | 2486 | 572 | 2 | 2 | 0 | 3 |
| Prokaryota | 9254 | 6856 | 8541 | 2667 | 602 | 3 | 2 | 0 | 4 |
| Yeast | 23 | 0 | 23 | 0 | 0 | 0 | 0 | 0 | 0 |
| Trypanosoma | 15 | 0 | 15 | 0 | 0 | 0 | 0 | 0 | 0 |
| Drosophila | 20 | 0 | 20 | 0 | 0 | 0 | 0 | 0 | 0 |
| Mouse | 3 | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 0 |
| Human | 23 | 0 | 23 | 0 | 0 | 0 | 0 | 0 | 0 |
| Eukaryota | 96 | 12 | 96 | 3 | 0 | 0 | 0 | 0 | 0 |
| Uncultured or unidentified | 2 | 1 | 2 | 1 | 0 | 0 | 0 | 0 | 0 |
Last updated: Mar 11 2010
back to topDeposited Structure Statistics for NYCOMPS Center
Number of Released X-Ray Structures: 8
Number of Released NMR Structures: 0
Total number of released structures from NYCOMPS center in the PDB: 8
Table 3: PDB Status Statistics for Structures from NYCOMPS
| PDB Status | Number of Structures |
| Total Deposited | 8 |
| Released | 8 |
| In Process | 0 |
| Last updated: Mar 11 2010 |
| Note 1: "Total Deposited" are all structures in the PDB including structures released to the public and structures that are in the process to be released("Released on Publication" , "Released on Certain Date", etc.). |
Table 4: List of Structures Deposited in the PDB by NYCOMPS
Total number of structures: 8
Structures of distinct targets: 41
1
A target may reference several PDB IDs
(example: structure of the same polypeptides with different ligands).
In this case only one structure is counted to compute number of structures of
distinct targets
Related PDB_ID(s): PDB_ID(s) associated with the same target in targetDB
| PDB_ID | Title | Target_id | Deposition Date | Released Date | PDB Status | Related PDB_ID in TargetDB |
| 3GI8 | crystal structure of apct k158a transporter bound to 7f11 monoclonal fab fragment | GO.9411 | 2009-03-05 | 2009-08-18 | REL | 3GI9 3GIA |
| 3K3F | crystal structure of the urea transporter from desulfovibrio vulgaris | GO.3782 | 2009-10-02 | 2009-11-17 | REL | 3K3G |
| 3GIA | crystal structure of apct transporter | GO.9411 | 2009-03-05 | 2009-08-18 | REL | none |
| 3K3G | crystal structure of the urea transporter from desulfovibrio vulgaris bound to 1,3-dimethylurea | GO.3782 | 2009-10-02 | 2009-11-17 | REL | none |
| 3KLY | pentameric formate channel | GO.190 | 2009-11-09 | 2009-12-15 | REL | 3KLZ |
| 3GI9 | crystal structure of apct transporter bound to 7f11 monoclonal fab fragment | GO.9411 | 2009-03-05 | 2009-08-18 | REL | none |
| 3KLZ | pentameric formate channel with formate bound | GO.190 | 2009-11-09 | 2009-12-15 | REL | none |
| 2QJU | crystal structure of an nss homolog with bound antidepressant | GO.3204 | 2007-07-09 | 2007-08-21 | REL | none |
Note 1: Last updated: Mar 11 2010
back to topSequence Redundancy Statistics
Table 5: Sequence Redundancy Statistics for NYCOMPS by Experimental Status
| Sequence Identity(%) | Novel Targets
Status: Selected |
Novel Targets Status: Cloned |
Novel Targets Status: Expressed |
Novel Targets Status: Purified |
Novel Targets Status: Crystallized |
Novel Targets Status: Crystal Structure | Novel Targets Status: in PDB |
| <100 | 6372 | 2945 | 2076 | 408 | 0 | 0 | 1 |
| <90 | 5915 | 2743 | 1985 | 397 | 0 | 0 | 1 |
| <70 | 4926 | 2288 | 1727 | 373 | 0 | 0 | 1 |
| <50 | 3249 | 1550 | 1287 | 315 | 0 | 0 | 1 |
| <30 | 816 | 493 | 483 | 169 | 0 | 0 | 1 |
| Last updated: 10-03-08 |
| Sequence redundancy is calculated by clustering analysis using BLASTClust program with similarity threshold set to percent of sequence identity. Please view detailed explanation of sequence redundancy calculations and BLASTClust threshold settings. Sequence redundancy calculations are based on comparison to all protein sequences in TargetDB which are in the same experimental status category and at least 20 amino acids long |
Table 6:Sequence Redundancy Statistics for Structures Released by NYCOMPS by Year
| Year | Released Structures | Number of Released Structures <30% Identity at Time of Release | Percent(%) of Released Structures <30% Identity(%) at Time of Release |
| 2007 | 1 | 0 | 0 |
| 2009 | 7 | 2 | 29 |
| Total | 8 | 2 | 25 |
| Last updated:10-03-11 |
| Sequence redundancy is calculated by clustering analysis using BLASTClust program with similarity threshold set to percent of sequence identity. Please view detailed explanation of sequence redundancy calculations and BLASTClust threshold settings. Sequence redundancy calculations are based on comparison to all protein sequences in the PDB which are at least 20 amino acids long |
