TargetDB Statistics Summary Report

Last updated: Mar 11 2010

• 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: 246866

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	174533	100.0	-	-	-
Expressed	122094	70.0	100.0	-	-
Soluble	46549	26.7	38.1	-	-
Purified	42798	24.5	35.1	100.0	-
Crystallized	14421	8.3	11.8	33.7	100.0
Diffraction-quality Crystals	7614	4.4	6.2	17.8	52.8
Diffraction	6534	3.7	5.4	15.3	45.3
NMR Assigned	2135	1.2	1.7	5.0	-
HSQC	3885	2.2	3.2	9.1	-
Crystal Structure	5148	2.9	4.2	12.0	35.7
NMR Structure	2034	1.2	1.7	4.8	-
In PDB1	7470	4.3	6.1	17.5	38
Work Stopped	33829	-	-	-	-
Test Target	94	-	-	-	-
Other	8139	-	-	-	-

Last updated: Mar 11 2010

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: Mar 11 2010

This graph is normalized relative to number of cloned targets in TargetDB.
Targets that progressed to status "Cloned" constitute 71% of TargetDB.

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Table 2: TargetDB Status Statistics 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	1218	208	794	553	249	55	37	18	52
Archaea	16622	1942	13077	9203	3865	1412	685	59	797
Bacteria	157562	19571	116706	87801	31150	11248	3863	497	4602
Prokaryota	174178	21513	129779	97000	35013	12659	4547	555	5397
Yeast	3054	543	1970	1689	1152	118	59	15	60
Plasmodium	4975	416	2783	1201	194	65	19	3	23
Trypanosoma	5287	70	3443	1757	292	58	9	0	8
Leishmania	8669	271	4181	2120	371	139	20	0	16
Arabidopsis	7790	3843	3814	1115	302	84	35	53	89
Rice	168	121	143	74	12	4	1	0	1
Worm	14460	2892	12225	5555	480	114	30	5	36
Drosophila	981	22	230	176	53	10	8	11	19
Mouse	6329	1300	4046	3210	1671	376	132	667	799
Human	16089	1954	8460	6731	3224	648	205	1197	1402
Eukaryota	66385	11370	40811	23031	7238	1592	533	1461	1985
Uncultured or unidentified	267	36	170	137	75	36	11	0	19

Last updated: Mar 11 2010

Note 1:   Total counts in this table may differ from total number of targets and structures. A target is counted in different organism specifications if:
- a target is mapped to different organisms
- a targtet is a hybrid complex (for example:a complex of human and mouse polypeptides)

Figure 2: Source Organisms in TargetDB

Last updated: Mar 11 2010

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Deposited Structure Statistics

Number of released X-Ray structures reported to TargetDB: 5969

Number of released NMR structures reported to TargetDB: 1865

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

Total number of released structures from worldwide SG Centers reported to TargetDB: 7837

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	8079	4875	379	152	2714
Released	7837	4652	371	148	2709
Release on Publication	8	1	2	0	5
Release on Certain Date	0	0	0	0	0
In Process	234	222	8	4	0

Last updated: Mar 11 2010

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: Mar 11 2010

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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	162049	116756	84468	31911	12006	4278	1945	6404
<90	149171	109736	79848	30469	11548	4103	1927	6204
<70	132694	99997	73384	28686	11194	4039	1813	6022
<50	104120	81765	60523	24699	10216	3822	1678	5617
<30	56795	48009	35313	16190	7608	3210	1478	4679

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 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	98	33	34
2001	73	24	33
2002	171	59	35
2003	413	156	38
2004	955	377	39
2005	1062	358	34
2006	1156	445	38
2007	1598	561	35
2008	1061	496	47
2009	1073	475	44
2010	168	81	48
Total	7828	3065	39

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

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

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

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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