TargetDB Statistics Summary Report

Last updated: Jul 2 2009

• Target Status Statistics
  • Table 1: TargetDB Status Statistics
  • Figure 1: Experimental Status in TargetDB
  • Table 2: TargetDB Status Statistics by Organisms
  • Figure 2: Source Organisms in TargetDB
• Deposited Structure Statistics
  • Table 3: PDB Status Statistics for Structural Genomics Structures
  • Figure 3: Structures Released by SG Centers by Year
• Sequence Redundancy Statistics
  • Table 4: TargetDB Sequence Redundancy Statistics by Experimental Status
  • Table 5: Sequence Redundancy Statistics for Structures Released by SG Centers in the PDB by Year
  • Figure 4: Comparison of Novel Structures with Total Number of Structures Released by SG Centers
• Links to Summary Statistics for Projects/Geographical Regions

Target Status Statistics

Total number of targets deposited by worldwide SG Centers in TargetDB: 222177

Table 1: TargetDB Status Statistics

Status	Total Number of Targets	(%) Relative to "Cloned" Targets	(%) Relative to "Expressed" Targets	(%) Relative to "Purified" Targets	(%) Relative to "Crystallized" Targets
Cloned	149354	100.0	-	-	-
Expressed	101435	67.9	100.0	-	-
Soluble	38556	25.8	38.0	-	-
Purified	36908	24.7	36.4	100.0	-
Crystallized	12834	8.6	12.7	34.8	100.0
Diffraction-quality Crystals	6505	4.4	6.4	17.6	50.7
Diffraction	5835	3.9	5.8	15.8	45.5
NMR Assigned	2075	1.4	2.0	5.6	-
HSQC	3861	2.6	3.8	10.5	-
Crystal Structure	4633	3.1	4.6	12.6	36.1
NMR Structure	1968	1.3	1.9	5.3	-
In PDB1	6811	4.6	6.7	18.5	38
Work Stopped	37080	-	-	-	-
Test Target	104	-	-	-	-
Other	10494	-	-	-	-

Last updated: Jul 2 2009

Note 1:   Number of targets with status "in PDB" may not be equal to number of structures determined by a project. A target may reference several PDB IDs (example: structure of the same polypeptides with different ligands). Multiple targets in TargetDB may identify the same PDB structure when a stucture is a result of collaboration between different centers and each center includes the target on its target list.

Figure 1: Experimental Status in TargetDB

Last updated: Jul 2 2009

This graph is normalized relative to number of cloned targets in TargetDB.
Targets that progressed to status "Cloned" constitute 67% of TargetDB.

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Table 2: TargetDB Status Statistics by Organism

Organism	Total Number1	Work Stopped	Cloned	Expressed	Purified	Crystallized	Crystal Structure	NMR Structure	In PDB2
Total Viruses	769	118	411	260	140	34	27	10	34
Archaea	15203	2348	11401	7904	3472	1326	635	52	740
Bacteria	135570	19122	95147	70874	26335	9902	3458	437	4042
Total Prokaryotes	150773	21470	106548	78778	29807	11228	4093	489	4782
Yeast	2759	681	1974	1368	810	120	60	14	58
Plasmodium	5201	335	2958	1263	201	69	20	0	20
Trypanosoma	6437	92	3975	1931	301	59	9	0	8
Leishmania	9599	288	4576	2211	404	146	21	0	17
Arabidopsis	8133	4965	4026	1194	341	78	37	54	92
Rice	136	101	128	62	13	4	1	0	1
Nematode	15175	3467	12741	5687	466	103	30	7	38
Fly	959	290	173	96	42	5	3	4	8
Mouse	2770	794	2155	1645	789	216	68	268	340
Human	14179	4033	7483	5297	2884	550	162	1086	1262
Other Eukaryotes	3016	448	1955	1409	520	152	82	15	98
Total Eukaryotes	68364	15494	42144	22163	6771	1502	493	1448	1942
Synthetic	4	0	4	4	4	1	1	2	3
Unknown	42	0	29	23	1	0	0	0	0
Total	219952	37082	149136	101228	36723	12765	4614	1949	6761

Last updated: Jul 2 2009

Note 1:   Total counts in this table may differ from total number of targets. If targtet is a hybrid complex
(for example:a complex of human and mouse polypeptides) it is counted in different organism classifications.
Note 2:   Number of targets with status "in PDB" may not be equal to number of structures determined by a project. A target may reference several PDB IDs (example: structure of the same polypeptides with different ligands). Multiple targets in TargetDB may identify the same PDB structure when a stucture is a result of collaboration between different centers and each center includes the target on its target list.

Figure 2: Source Organisms in TargetDB

Last updated: Jul 2 2009

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Deposited Structure Statistics

Number of released X-Ray structures reported to TargetDB: 5321

Number of released NMR structures reported to TargetDB: 1781

Number of released Cryo-Electron Microscopy structures reported to TargetDB: 3

Total number of released structures from worldwide SG Centers reported to TargetDB: 7105

View list of all reported to TargetDB structures deposited by worldwide SG Centers to the PDB

Table 3: PDB Status Statistics for Structural Genomics Structures

Status	All Centers	PSI Centers	Non-PSI SG Centers in North America	SG Centers in Europe	SG Centers in Asia
Total Deposited	7367	4296	252	138	2708
Released	7105	4068	243	134	2689
Release on Publication	19	0	3	0	16
Release on Certain Date	2	1	0	0	1
In Process	241	227	8	4	2

Last updated: Jul 2 2009

1:   Some PDB IDs are cross referenced by different centers. Example: PDB_id 106Y is associated with SPINE and TB centers. Therefore difference between number of structures in "ALL Centers" column and direct sum of number of structures from projects/geographical regions can be observed.

2:   "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.).

Figure 3: Structures Released by SG Centers by Year

Last updated: Jul 2 2009

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Sequence Redundancy Statistics

Table 4: TargetDB Sequence Redundancy Statistics 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: NMR Structure	Novel Targets Status: in PDB
<100	150190	109891	75052	29127	10881	3944	1880	5994
<90	138310	103316	71081	27794	10451	3774	1862	5797
<70	124089	94424	65769	26228	10152	3719	1740	5614
<50	98933	77779	55003	22651	9313	3526	1582	5215
<30	50434	43342	31649	14512	6970	2945	1169	4114

Last updated: 09-04-28

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 5: Sequence Redundancy Statistics for Structures Released by SG Centers in the PDB by Year

Year	Released Structures	Number of Released Structures <30% Sequence Identity at Time of Release	Percent(%) of Released Structures <30% Sequence Identity at Time of Release
<= 2000	97	34	35
2001	73	25	34
2002	171	59	35
2003	414	157	38
2004	955	383	40
2005	1062	366	34
2006	1157	452	39
2007	1597	572	36
2008	1063	509	48
2009	516	236	46
Total	7105	2793	39

Last updated: 09-07-02

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

Figure 4: Comparison of Novel Structures with Number of Structures Released By SG Centers

Last updated: 09-07-02

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

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Summary Statistics Reports by Project or Geographical Region:

• PSI Centers
• Other Structural Genomics Centers in North America
• Structural Genomics Centers in Europe
• Structural Genomics Centers in Asia