Metrics | tracking milestones made by PSI:Biology

Last updated: June 28, 2017

The PSI:Biology Goals and Milestone Committee was charged with determining a list of metrics that best convey the progress and impact of the PSI:Biology Network.
Click a category name to jump down to active tabulations. Collected PSI-1 and PSI-2 statistics can be viewed on the previous Metrics site.
To learn how each metric is calculated, click on its data source icon (e.g. TT ) nearest to its column heading.



1. Quantitative Metrics

These tables provide a summary of the PSI:Biology targets being studied by the High-throughput and Membrane Protein Centers, as determined from depositions to TargetTrack or the PDB.

Table 74348. Numbers of targets in the PSI:Biology pipeline and the number of structures solved. (Metrics items 1.1-1.8)

Table 1 : Metrics
TT TT TT TT TT TT
PDB
PDB
Center Total Cloned Expressed Purified Structure Studies
(X-ray/NMR/EM)
In PDB Structures
In PDB
JCSG 9809 9758 8735 3323 2299 / 181 / 0 484 516
MCSG 8051 5991 2268 2103 1114 / 3 / 0 340 579
NESG 6696 4979 4166 1805 920 / 796 / 0 263 327
NYSGRC 25122 17996 4090 2902 1887 / 13 / 0 228 359
CSMP 168 147 124 26 17 / 0 / 0 1 5
GPCR 826 50 38 30 18 / 0 / 0 16 52
MPID 55 49 24 30 10 / 1 / 0 0 0
MPSBC 141 107 93 26 23 / 0 / 1 1 3
MPSbyNMR 14 14 14 12 0 / 11 / 0 3 8
NYCOMPS 5755 3134 1017 473 3 / 0 / 0 2 37
TEMIMPS 100 81 65 52 0 / 0 / 23 1 3
TMPC 253 137 115 27 18 / 0 / 0 0 0
TransportPDB 592 331 297 127 10 / 0 / 0 0 0

Table 74349. Number of PSI:Biology targets classified by Target Category (Metrics items 1.9 - 1.10) TT

Table 2 : Metrics
TT TT TT TT TT TT
Center PSI Biology
Partnership
Biomedical Structural
Coverage
Community
Nominated
Metagenomic Membrane
Protein
JCSG 2151 (22%) 6253 (64%) 4431 (46%) 692 (8%) 27 (1%) 0
MCSG 2069 (26%) 3963 (50%) 3411 (43%) 1428 (18%) 769 (10%) 100 (2%)
NESG 1395 (21%) 4212 (63%) 1777 (27%) 874 (14%) 49 (1%) 0
NYSGRC 2176 (9%) 11466 (46%) 4500 (18%) 6980 (28%) 0 0
CSMP 113 (68%) 168 (100%) 0 0 0 166 (99%)
GPCR 5 (1%) 826 (100%) 0 17 (3%) 0 826 (100%)
MPID 0 55 (100%) 0 0 0 55 (100%)
MPSBC 0 0 0 0 0 141 (100%)
MPSbyNMR 0 2 (15%) 11 (79%) 0 0 14 (100%)
NYCOMPS 0 0 0 256 (5%) 0 5755 (100%)
TEMIMPS 0 0 0 0 0 100 (100%)
TMPC 0 110 (44%) 139 (55%) 144 (57%) 1 (1%) 252 (100%)
TransportPDB 0 592 (100%) 571 (97%) 11 (2%) 0 592 (100%)

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2. Structure Determination

This section counts the number of different structural and biological topics targeted by the PSI:Biology network as categorized in TargetTrack.

Table 74350. Types of protein targets among the PSI:Biology structures (Metrics item 2.1)

Table 3 : Metrics
Type of Protein Target No. of structures Source
Single-domain proteins 1021 SBKB
Multidomain proteins 901 SBKB
Oligomeric proteins 953 PDB
Membrane proteins 116 PDB
Eukaryotic proteins 257 PDB
Protein-protein complexes 43 PDB
Protein-nucleic acid complexes 17 PDB
Protein-ligand complexes 1403 PDB
de novo/designed proteins 61 PDB

2.2 Structure Determination Methods PDB

Table 74351. Classifies PSI:Biology Structure by their structure determination method.

Total PSI:Biology Structures by methodX-rayNMROther87.3%
MethodsStructures
X-ray1,601
NMR230
SAXS0
EM1
Other1
Table 5 : Metrics
Year X-ray NMR SAXS EM Other Total
2010 111 20 0 0 0 131
2011 315 57 0 0 0 372
2012 344 59 0 1 0 404
2013 395 43 0 0 1 439
2014 272 26 0 0 0 298
2015 164 25 0 0 0 189
Total 1601 230 0 1 1 1833

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3. Network Building

One of the goals of the PSI:Biology program is to be a collaborative network for the greater biological community to rely on for structures and resources. This section counts the level of collaboration within the PSI:Biology Network and beyond it.

3.1 Collaboration

3.1.2 External to PSI

3.1.2.3 (Table 74352) Collaborations created by Community-nominated Target nominations SBKB

Table 6 : Metrics
Center Name No. of
Collaborations
HTP centers
JCSG 30
MCSG 24
NESG 36
NYSGRC 15
Participating MP centers
CSMP 0
GPCR 14
MPSBC 0
NYCOMPS 11
TMPC 21
TransportPDB 1

4. Experimental Data Resources

The PSI:Biology Network makes all of its research resources available to the public. The following resource counts come from center depositions and TargetTrack.

4.1 (Table 74353) Protocols used by the PSI:Biology program. TT

Table 8 : Metrics
Center Expression Purification Crystallization
HTP centers
JCSG 3 2 3
MCSG 7 10 9
NESG 2 1 1
NYSGRC 53 37 4
MP centers
CSMP 2 0 0
GPCR 1 0 0
MPID 3 7 6
MPSBC 4 3 5
MPSbyNMR 3 4 0
NYCOMPS 6 6 3
TEMIMPS 53 28 21
TMPC 9 10 2
TransportPDB 0 1 0
Biology Partners
MPP 9 6 3
NatPro 1 5 2

4.2 (Table 74354) Available PSI:Biology clones. Mr

Table 9 : Metrics
Center Name Type PSI-I+PSI-II PSI:Biology Clones
JCSG HTP 24412 2800
MCSG HTP 9374 6713
NESG HTP 10675 8432
NYSGRC HTP 10690 5312
Total HTP centers 55151 23257
CSMP MP 77 0
GPCR MP N/A 67
MPID MP N/A 180
MPSBC MP N/A 52
MPSbyNMR MP N/A 2
NYCOMPS MP 2507 697
TEMIMPS MP N/A 15
TMPC MP N/A 68
TransportPDB MP N/A 44
Total MP centers 2584 1125
CEBS BP N/A 0
CELLMAT BP N/A 0
CHSAM BP N/A 0
IFN BP N/A 0
MPP BP N/A 66
MTBI BP N/A 0
NatPro BP N/A 7
NPCXstals BP N/A 0
STEMCELL BP N/A 0
TCELL BP N/A 0
PCSEP BP N/A 0
TJMP BP N/A 84
Total BP centers N/A 157

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5. Technologies

The PSI:Biology Network also develops new technologies to overcome bottlenecks in the high-throughput protein production and structural determination pipeline. During PSI:Biology, technological developments are mainly underway for the membrane protein-focused centers and the high-throughput centers. This data is calculated from the PSI Technology Portal.

5.1 - 5.5 (Table 74355) Technologies from HTP and Membrane Protein Centers. Tech Portal

Table 10 : Metrics
Tech Portal Tech Portal Tech Portal Tech Portal Tech Portal Tech Portal coming soon
Center PSI-I+PSI-II Devices Software & Servers Protein Complexes Eukaryotic Proteins Membrane Proteins PTMs
HTP centers
JCSG 39 0 6 3 2 2
MCSG 32 0 5 8 0 0
NESG 38 2 9 7 1 1
NYSGRC 9 3 4 2 1 1
Membrane centers
CSMP 10 3 0 0 0 2
GPCR N/A 0 2 1 0 2
MPID N/A 1 0 0 0 1
MPSBC N/A 2 0 0 0 1
MPSbyNMR N/A 4 1 0 0 5
NYCOMPS 1 2 0 1 0 4
TEMIMPS N/A 6 5 0 0 2
TMPC N/A 2 0 0 0 17
TransportPDB N/A 0 0 0 0 0

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6. Publications

Below is a tabulation of the number, citation count, and impact of PSI:Biology publications, along with the number of times a center's PDB structure has been downloaded from all PDB sites. The download numbers exclude full PDB archive downloads. This data is collected from the PSI Publications Portal and the wwPDB site.

(Table 74356) Publications and statistics

Table 11 : Metrics
Pubs Portal Pubs Portal Pubs Portal PDB
Center Names No.
Publications
No. Times
Article Cited
Total
Journal Impact
No. of PDB
downloads
JCSG 101 2595 771.93 3388318
MCSG 87 1155 326.53 2559728
NESG 172 2657 1033.31 2470402
NYSGRC 46 1040 310.72 2052750
CSMP 23 825 232.3 25567
GPCR 57 7423 1033.87 1100263
MPID 27 2577 304.64 0
MPSBC 7 136 62.87 8934
MPSbyNMR 33 1449 303.75 56323
NYCOMPS 37 1255 578.05 58007
TEMIMPS 27 466 204.37 10680
TMPC 10 106 35.86 0
TransportPDB 7 221 37.6 0
CEBS 7 245 71.71 36093
CELLMAT 11 239 47.83 13095
CHSAM 28 1687 182.14 0
IFN 5 104 36.3 183456
MPP 25 330 127.25 74913
MTBI 7 4028 38.37 214998
NatPro 17 180 74.06 194457
NPCXstals 2 10 2.81 18499
STEMCELL 6 84 52.06 113444
TCELL 1 15 0.0 303296
PCSEP 14 142 49.47 100912
TJMP 5 86 20.56 0

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