Statistics Summary Report for PSI Centers

Last updated: Mar 11 2010

PSI-2 Centers:

|ATCG3D| |CESG| |CHTSB| |CSMP| |JCSG| |ISFI| |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: 227169

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	158810	100.0	-	-	-
Expressed	109865	69.2	100.0	-	-
Soluble	38296	24.1	34.9	-	-
Purified	34375	21.6	31.3	100.0	-
Crystallized	11032	6.9	10.0	32.1	100.0
Diffraction-quality Crystals	5551	3.5	5.1	16.1	50.3
Diffraction	4478	2.8	4.1	13.0	40.6
NMR Assigned	678	0.4	0.6	2.0	-
HSQC	2359	1.5	2.1	6.9	-
Crystal Structure	3410	2.1	3.1	9.9	30.9
NMR Structure	609	0.4	0.6	1.8	-
In PDB1	4248	2.7	3.9	12.4	33
Work Stopped	33417	-	-	-	-
Test Target	93	-	-	-	-
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: Target Experimental Status for PSI Centers

Last updated: Mar 11 2010

This graph is normalized relative to number of cloned targets in TargetDB.
Targets that progressed to status "Cloned" constitute 70% 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 PDB2
Viruses	844	205	506	418	193	35	19	13	34
Archaea	15000	1928	11501	8044	2825	801	259	58	372
Bacteria	144863	19241	107132	80798	26832	9193	2821	452	3408
Prokaryota	159857	21169	118629	88838	29655	9993	3079	509	3778
Yeast	2678	524	1659	1423	1044	101	42	11	52
Plasmodium	4954	416	2771	1192	187	62	16	0	17
Trypanosoma	5285	70	3441	1755	291	58	9	0	8
Leishmania	8664	271	4177	2118	369	139	20	0	16
Arabidopsis	7748	3842	3772	1073	264	82	35	21	57
Rice	168	121	143	74	12	4	1	0	1
Worm	14457	2892	12223	5553	478	114	30	3	34
Drosophila	948	22	205	154	36	5	4	2	6
Mouse	4923	1288	2712	1900	490	143	44	13	64
Human	13204	1933	5803	4136	1070	188	69	36	124
Eukaryota	61527	11298	36558	19116	4245	904	282	85	399
Uncultured or unidentified	238	33	146	126	69	34	10	0	17

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 PSI Centers

Last updated: Mar 11 2010 back to top

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Deposited Structure Statistics for PSI Centers

Number of Released X-Ray Structures: 4207

Number of Released NMR Structures: 445

Total number of released structures from PSI Centers in the PDB: 4652

Table 3: PDB Status Statistics for Structures from PSI Centers

PDB Status	ATCG3D	BSGC	CESG	CHTSB	CSMP	JCSG	ISFI	MCSG	NESGC	NYCOMPS	NYSGXRC	SECSG	SGPP	TB	Total
Total Deposited	14	88	145	12	12	1001	31	1188	828	8	908	92	41	515	4875
Released	14	88	144	12	9	985	13	1167	812	8	893	92	41	382	4652
In Process	0	0	1	0	2	16	18	21	16	0	15	0	0	133	222

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.).

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: Mar 11 2010

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	149922	106971	76921	26099	9564	3108	570	3813
<90	138775	101199	73186	25148	9299	3081	569	3782
<70	123781	92484	67392	23802	9031	3041	564	3741
<50	98049	76411	56058	20798	8364	2939	545	3601
<30	54415	45794	33386	14183	6558	2625	521	3167

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 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	22	37
2001	47	18	38
2002	113	45	40
2003	228	108	47
2004	557	252	45
2005	494	255	52
2006	693	373	54
2007	753	448	60
2008	706	448	63
2009	850	455	54
2010	143	80	56
Total	4643	2504	54

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 PSI Centers by Year

Note 1:  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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