TargetDB Statistics Summary Report

Last updated: Feb 2 2012

• 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 Biology Structures
• Figure 3: Structures Released by Contributing Centers by Year
• Sequence Redundancy Statistics
• Table 4: TargetDB Sequence Redundancy Statistics by Experimental Status
• Table 5: Sequence Redundancy Statistics for Structures Released by Contributing Centers in the PDB by Year
• Figure 4: Comparison of Novel Structures with Total Number of Structures Released by Contributing Centers
• Links to Summary Statistics for Projects/Geographical Regions

Target Status Statistics

Total number of targets deposited by worldwide Contributing Centers in TargetDB: 290110

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	199435	100.0	-	-	-
Expressed	126893	63.6	100.0	-	-
Soluble	36626	18.4	28.9	-	-
Purified	46994	23.6	37.0	100.0	-
Crystallized	15017	7.5	11.8	32.0	100.0
Diffraction-quality Crystals	7290	3.7	5.7	15.5	48.5
Diffraction	7781	3.9	6.1	16.6	51.8
NMR Assigned	2287	1.1	1.8	4.9	-
HSQC	3471	1.7	2.7	7.4	-
Crystal Structure	5199	2.6	4.1	11.1	34.6
NMR Structure	2162	1.1	1.7	4.6	-
In PDB1	8878	4.5	7.0	18.9	45
Work Stopped	95127	-	-	-	-
Test Target	103	-	-	-	-
Other	11281	-	-	-	-

Last updated: Feb 2 2012

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: Feb 2 2012

This graph is normalized relative to number of cloned targets in TargetDB.
Targets that progressed to status "Cloned" constitute 69% 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 PDB
Viruses	1443	463	861	667	284	66	42	18	64
Archaea	18351	6721	14200	8816	3909	1324	608	63	835
Bacteria	184627	65088	133588	88169	34283	11546	3858	569	5750
Prokaryota	202973	71808	147785	96982	38191	12870	4466	631	6584
Yeast	3231	1447	2503	1766	1063	120	49	16	64
Plasmodium	4978	425	2761	1194	193	65	20	3	23
Trypanosoma	5568	90	3479	1786	294	58	10	0	10
Leishmania	8766	272	4193	2127	373	142	21	0	17
Arabidopsis	7792	6518	3826	1138	301	84	35	53	89
Rice	176	134	148	75	12	4	1	0	1
Worm	14510	3235	12257	5575	467	122	26	6	39
Drosophila	1144	579	336	285	67	21	19	12	31
Mouse	9588	2784	6136	4736	2008	481	157	685	837
Human	25167	6611	12932	10364	3887	866	290	1231	1510
Eukaryota	79542	21347	46929	27507	8071	1938	660	1503	2170
Uncultured or unidentified	411	124	296	182	112	35	10	0	24

Last updated: Feb 2 2012

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 target is a hybrid complex (for example:a complex of human and mouse polypeptides).

Figure 2: Source Organisms in TargetDB

Last updated: Feb 2 2012

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Deposited Structure Statistics

Number of released X-Ray structures reported to TargetDB: 7511

Number of released NMR structures reported to TargetDB: 2009

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

Total number of released structures from worldwide Contributing Centers reported to TargetDB: 9523

View list of all structures deposited by worldwide Contributing Centers to the PDB, as reported to TargetDB.

Table 3: PDB Status Statistics for Structural Biology Structures

Status	All Centers	PSI Centers	Non-PSI Contributing Centers in North America	Contributing Centers in Europe	Contributing Centers in Asia
Total Deposited	9794	6042	909	134	2713
Released	9523	5791	894	130	2713
Release on Publication	4	1	2	0	0
Release on Certain Date	1	1	0	0	0
In Process	266	249	13	4	0

Last updated: Feb 2 2012

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 Contributing Centers by Year

Last updated: Feb 2 2012

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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	206402	149520	98466	39343	13307	4494	2102	8105
<98	227700	144873	95602	38314	12901	4311	2096	7909
<95	193372	142681	94301	37943	12832	4301	2091	7891
<90	188106	139760	92583	37462	12760	4281	2083	7859
<70	164126	124799	83350	34886	12229	4153	1960	7587
<50	125311	98915	66929	29557	11072	3828	1782	6960
<40	96604	78348	53572	24854	9793	3473	1613	6334
<30	58408	49983	35250	17646	7863	2996	1342	5271

Last updated: 12-01-10

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 Contributing 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	100	32	32
2001	73	23	32
2002	171	54	32
2003	416	141	34
2004	958	363	38
2005	1065	347	33
2006	1161	428	37
2007	1610	538	33
2008	1107	485	44
2009	1130	456	40
2010	986	341	35
2011	693	166	24
2012	41	7	17
Total	9511	3381	36

Last updated: 12-02-02

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 Contributing Centers

Last updated: 12-02-02

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 Biology Centers in North America
• Structural Biology Centers in Europe
• Structural Biology Centers in Asia