Statistics Summary Report for PSI Centers

Last updated: Feb 2 2012

PSI-2 Centers:

|ATCG3D| |CESG| |CHTSB| |CSMP| |ISFI| |JCSG| |MCSG| |NESG| |NYCOMPS| |NYSGXRC|

PSI-1 Centers:

|BSGC| |SECSG| |SGPP| |TB|

• Target Status Statistics
• Table 1: Status Statistics for PSI Centers
• Figure 1: Target Experimental Status for PSI Centers
• Table 2: Status Statistics for PSI Centers by Organisms
• Figure 2: Source Organisms at PSI Centers
• Deposited Structure Statistics
• Table 3: PDB Status Statistics for Structures from PSI Centers
• Figure 3: Structures Released by PSI Centers by Year
• Table 4: List of Structures Deposited by PSI Centers in the PDB
• Sequence Redundancy Statistics
• Table 5: Sequence Redundancy Statistics for PSI Centers by Experimental Status
• Table 6: Sequence Redundancy Statistics for Structures Released by PSI Centers in the PDB by Year
• Figure 4: Comparison of Novel Structures with Number of Structures Released by PSI Centers by Year

Target Status Statistics

Total number of targets deposited by PSI Centers to TargetDB: 260303

Table 1: Status Statistics for PSI Centers

Status	Total Number of Targets	(%) Relative to "Cloned" Targets	(%) Relative to "Expressed" Targets	(%) Relative to "Purified" Targets	(%) Relative to "Crystallized" Targets
Cloned	176125	100.0	-	-	-
Expressed	107113	60.8	100.0	-	-
Soluble	26015	14.8	24.3	-	-
Purified	36145	20.5	33.7	100.0	-
Crystallized	10637	6.0	9.9	29.4	100.0
Diffraction-quality Crystals	4850	2.8	4.5	13.4	45.6
Diffraction	5148	2.9	4.8	14.2	48.4
NMR Assigned	816	0.5	0.8	2.3	-
HSQC	1917	1.1	1.8	5.3	-
Crystal Structure	2844	1.6	2.7	7.9	26.7
NMR Structure	724	0.4	0.7	2.0	-
In PDB1	5166	2.9	4.8	14.3	42
Work Stopped	94254	-	-	-	-
Test Target	102	-	-	-	-
Other	8179	-	-	-	-

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: Target Experimental Status for PSI Centers

Last updated: Feb 2 2012

This graph is normalized relative to number of cloned targets in TargetDB.
Targets that progressed to status "Cloned" constitute 68% of TargetDB.

Table 2: Status Statistics for PSI Centers by Organism

These statistics is 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	908	456	499	394	199	34	16	13	39
Archaea	16440	6707	12346	7504	2788	705	174	62	402
Bacteria	163578	64342	117372	74443	27894	8674	2306	514	4175
Prokaryota	180013	71048	129715	81944	30681	9379	2480	575	4576
Yeast	2856	1428	2188	1500	956	103	32	12	56
Plasmodium	4881	424	2732	1181	185	61	17	0	17
Trypanosoma	5304	83	3443	1755	290	57	9	0	9
Leishmania	8681	271	4184	2122	371	140	21	0	17
Arabidopsis	7745	6517	3781	1095	262	82	35	21	57
Rice	170	134	144	73	12	4	1	0	1
Worm	14504	3235	12252	5570	464	122	26	4	37
Drosophila	1088	579	289	246	39	5	4	3	7
Mouse	8078	2772	4761	3383	823	244	65	34	101
Human	21565	6585	10139	7655	1670	359	115	70	193
Eukaryota	72723	21227	42055	23048	4844	1108	323	124	495
Uncultured or unidentified	340	118	237	138	88	28	4	0	17

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 PSI Centers

Last updated: Feb 2 2012

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Deposited Structure Statistics for PSI Centers

Number of Released X-Ray Structures: 5213

Number of Released NMR Structures: 578

Total number of released structures from PSI Centers in the PDB: 5791

Table 3: PDB Status Statistics for Structures from PSI Centers

PDB Status	ATCG3D	BSGC	CESG	CHTSB	CSMP	GPCR	ISFI	JCSG	MCSG	MPID	MPP	MPSBC	MPSBYNMR	NESG	NYCOMPS	NYSGRC	NYSGXRC	SECSG	SGPP	TB	TEMIMPS	TMPC	TRANSPORTPDB	Total
Total Deposited	22	88	154	16	12	5	124	1256	1468	0	0	0	1	1022	26	82	1032	92	41	617	0	0	0	6042
Released	22	88	152	16	12	5	13	1250	1463	0	0	0	1	1020	26	81	1032	92	41	493	0	0	0	5791
In Process	0	0	2	0	0	0	111	6	4	0	0	0	0	1	0	1	0	0	0	124	0	0	0	249

Last updated: Feb 2 2012

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.).

Note 2:  Some PDB IDs are cross referenced by different centers. Therefore difference between "Total" number of structures and direct sum of number of structures from individual centers can be observed.

Figure 3: Structures Released by PSI Centers by Year

Last updated: Feb 2 2012

Sequence Redundancy Statistics

Table 5: Sequence Redundancy Statistics for PSI Centers 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	184506	131815	82968	30940	9799	2712	713	5024
<98	206649	128553	81163	30396	9610	2693	712	4997
<95	174766	126782	80168	30126	9562	2688	711	4990
<90	170589	124432	78874	29791	9514	2678	711	4977
<70	150586	112257	71923	28110	9207	2615	707	4894
<50	116834	90586	59158	24514	8591	2522	687	4687
<40	91306	72913	48468	21309	7910	2410	669	4479
<30	55605	47002	32492	15606	6612	2201	642	3945

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 6: Sequence Redundancy Statistics for Structures Released by PSI Centers 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
<= 2000	59	23	39
2001	47	17	36
2002	113	41	36
2003	229	96	42
2004	558	244	44
2005	496	247	50
2006	692	359	52
2007	760	430	57
2008	751	440	59
2009	910	439	48
2010	741	326	44
2011	398	148	37
2012	25	6	24
Total	5779	2816	49

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 PSI Centers by Year

Note 1:  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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