Metrics Describing Progress of the Protein Structure Initiative

Updated March 01, 2010

I. Progress of the PSI
• PDB deposition statistics
• Numbers of experimental structures from PSI
II. Number of Experimental Structures and Residues
• Structures determined in PSI-1
• Structures determined in PSI-2
III. Impact and Classification of Structures
• Classification of PSI-2 structures
• Classification of PSI-2 structures by organism
• Detailed PSI-2 structure counts for eukaryotes
• Detailed PSI-2 structure counts for prokaryotes
• Detailed PSI-2 structure counts for other organisms
IV. Novel Modeling Leverage
• Leverage provided by PSI-2 structures
V. Biological Theme Targets & Structures
• Biological Theme Targets & Structures by PSI Center
• Biomedical Targets & Structures by PSI Center
• Metagenomic Targets & Structures by PSI Center
• Community Nominated Targets & Structures by PSI Center
VI. PSI PFAM Domain Family Covarage
• PFAM Domain Family Covarage

Glossary of Terms

• BIG: BioInformatics Group. A team of bioinformaticians from PSI-2 large-scale production centers that coordinate efforts of target selection and progress evaluation
• ALL-PSI: All PSI centers (PSI-1 and PSI-2)
• ALL PDB: Entire Protein Data Bank
• PSI-1: The pilot phase of the protein structure initiative (PSI) ran from 09-01-2000 to 06-30-2005
• PSI-2: The production phase of the protein structure initiative (PSI) (07-01-2005 - ongoing). Statistics on this page reflect PSI-2 data deposited after 07-01-2005 and released before 03-01-2010
• LSC: are the four Protein Structure Initiative(PSI) large-scale production centers; namely MCSG, JCSG, NESG, and NYSGXRC
• Total Structures: Total number of structures in the PDB at the time of deposition. This includes multiple structures of the same protein sequence determined by different methods (i.e., NMR versus X-ray crystallography), in different crystal forms, different solution conditions, or bound to different ligands.
• Distinct Structures: Total number of structures with non-redundant sequences less then 98% sequence identity
• Distinct Residues: Total number of residues in structures with non-redundant sequences less 98% sequence identity
• Novel Structures: Total number of novel structures with less than 30% sequence identity to an existing structure at the time of PDB deposition
• Novel Residues: Total number of residues in structures with less than 30% sequence identity to an existing structure at the time of PDB deposition
• X-Ray Structures: Total number of structures determined using X-Ray crystallography
• NMR Structures: Total number of structures determined using NMR methods
• Membrane Proteins: Total number of structures of membrane proteins
• Eukaryotic Proteins: Total number of structures from eukaryotic organisms
• Prokaryotic Proteins: Total number of structures from prokaryotic organisms
• Human Proteins: Total number of structures of human proteins
• Other Proteins: Total number of structures of viral and unknown source proteins

I. Progress of the PSI

PDB deposition statistics

PSI grant period	LSC	ALL-PSI
PSI-2 grant year 2005	419	456
PSI-2 grant year 2006	620	700
PSI-2 grant year 2007	681	717
PSI-2 grant year 2008	796	818
PSI-2 grant year 2009	447	470
PSI-2 current depositions	2963	3161
PSI-1+PSI-2	3831	4544

PSI-2 grant year 2005:
PSI-2 structures deposited after July 1, 2005; released before June 30, 2006
PSI-2 grant year 2006:
PSI-2 structures deposited after July 1, 2006; released before June 30, 2007
PSI-2 grant year 2007:
PSI-2 structures deposited after July 1, 2007; released before July 1, 2008
PSI-2 grant year 2008:
PSI-2 structures deposited after July 1, 2008; released before July 1, 2009
PSI-2 grant year 2009:
PSI-2 structures deposited after July 1, 2009; released before July 1, 2010
PSI-2 current depositions:
PSI-2 structures deposited after July 1, 2005; released before March 01, 2010
PSI-1 + PSI-2:
All PSI structures released before March 01, 2010

Numbers of experimental structures from PSI

Start of PSI Deposition:
Sep 2000: Structures deposited before PSI grant initiation (2000-09-01)

Each subsequent bar shows the total number of PSI structures deposited as of the First of each indicated date.

For example, there were 97 PSI-derived structures deposited as of September 1, 2001.

II. Number of Experimental Structures and Residues

Structures determined in PSI-1

Center	Total Structures	Distinct Structures	Distinct Residues	Novel Structures	Novel Residues
LSC	868	767	174843	458	100522
ALL-PSI-1	1383	1127	259397	631	138343
ALL PDB	34141	11505	2784172	4658	1133938

Calculations in this table are based on PDB data deposited before July 1, 2005

Structures determined in PSI-2

Center	Total Structures	Distinct Structures	Distinct Residues	Novel Structures	Novel Residues
LSC	2963	2708	614963	1794	402872
ALL-PSI-2	3161	2795	635617	1848	415064
ALL PDB	29439	11297	2781889	4658	1102275

Calculations in this table are based on PDB data deposited after July 1, 2005 and released before March 01, 2010.

III. Impact and Classification of PSI-2 Structures

Calculations in this section are based on PDB data deposited after July 1, 2005 and released before March 01, 2010.

Classification of PSI-2 structures

Center	Total Structures	X-ray	NMR	Membrane Proteins	Eukary- otes	Human	Other	Prokary- otes
LSC	2963	2679	284	18	143	72	38	2782
ALL-PSI-2	3161	2848	313	43	294	114	42	2827

Classification of PSI-2 structures by organism

Eukaryotes Total	294
Prokaryotes Total	2827
Other Organisms Total	42

Detailed PSI-2 structure counts for eukaryotes

Eukaryotes Total	294
Aequorea victoria	1
Anopheles gambiae	2
Arabidopsis thaliana	56
Aspergillus fumigatus	1
Aspergillus oryzae	2
Babesia bovis	1
Bos taurus	3
Brugia malayi	1
Caenorhabditis elegans	10
Candida albicans	1
Coccidioides immitis	1
Cyanidioschyzon merolae	1
Danio rerio	7
Drosophila melanogaster	3
Encephalitozoon cuniculi	4
Engyodontium album	1
Entamoeba histolytica	1
Galdieria sulphuraria	7
Gibberella zeae	2
Homo sapiens	114
Methanocaldococcus jannaschii	1
Mus musculus	32
Oncorhynchus mykiss	1
Oryza sativa	1
Pentadiplandra brazzeana	1
Plasmodium falciparum	1
Rana pipiens	2
Rattus norvegicus	4
Saccharomyces cerevisiae	22
Schizosaccharomyces pombe	2
Solanum lycopersicum	1
Spinacia oleracea	1
Sus scrofa	1
Toxoplasma gondii	3
Trypanosoma brucei	1
Xenopus laevis	1

Detailed PSI-2 structure counts for prokaryotes

Prokaryotes Total

2827

Genus: Acidithiobacillus 4 Acidithiobacillus ferrooxidans 4 Genus: Acidothermus 1 Acidothermus cellulolyticus 1 Genus: Acinetobacter 8 Acinetobacter baumannii 1 Acinetobacter calcoaceticus 1 Acinetobacter sp. 6 Genus: Actinobacillus 1 Actinobacillus succinogenes 1 Genus: Aeromonas 2 Aeromonas hydrophila 1 Aeromonas salmonicida 1 Genus: Aeropyrum 5 Aeropyrum pernix 5 Genus: Agrobacterium 94 Agrobacterium tumefaciens 94 Genus: Alcanivorax 2 Alcanivorax borkumensis 2 Genus: Alkaliphilus 2 Alkaliphilus metalliredigens 2 Genus: Allochromatium 1 Allochromatium vinosum 1 Genus: Alteromonas 1 Alteromonas macleodii 1 Genus: Anabaena 23 Anabaena sp. 1 Anabaena variabilis 22 Genus: Aquifex 6 Aquifex aeolicus 6 Genus: Archaeoglobus 56 Archaeoglobus fulgidus 56 Genus: Arthrobacter 7 Arthrobacter aurescens 1 Arthrobacter sp. 6 Genus: Aurantimonas 1 Aurantimonas sp. 1 Genus: Azoarcus 1 Azoarcus sp. 1 Genus: Azotobacter 2 Azotobacter vinelandii 2 Genus: Bacillus 241 Bacillus anthracis 11 Bacillus cereus 47 Bacillus clausii 2 Bacillus cytotoxicus 1 Bacillus halodurans 52 Bacillus licheniformis 1 Bacillus stearothermophilus 1 Bacillus subtilis 115 Bacillus thuringiensis 11 Genus: Bacteroides 154 Bacteroides fragilis 47 Bacteroides thetaiotaomicron 81 Bacteroides uniformis 1 Bacteroides vulgatus 25 Genus: Bartonella 5 Bartonella henselae 5 Genus: Bdellovibrio 2 Bdellovibrio bacteriovorus 2 Genus: Bifidobacterium 7 Bifidobacterium adolescentis 5 Bifidobacterium longum 2 Genus: Blastochloris 1 Blastochloris viridis 1 Genus: Bordetella 41 Bordetella bronchiseptica 18 Bordetella parapertussis 13 Bordetella pertussis 10 Genus: Bradyrhizobium 2 Bradyrhizobium japonicum 2 Genus: Burkholderia 29 Burkholderia mallei 4 Burkholderia phymatum 1 Burkholderia phytofirmans 2 Burkholderia pseudomallei 5 Burkholderia thailandensis 3 Burkholderia xenovorans 14 Genus: Campylobacter 9 Campylobacter jejuni 9 Genus: Carboxydothermus 2 Carboxydothermus hydrogenoformans 2 Genus: Caulobacter 12 Caulobacter crescentus 6 Caulobacter vibrioides 6 Genus: Chlamydia 1 Chlamydia trachomatis 1 Genus: Chlamydophila 1 Chlamydophila abortus 1 Genus: Chlorobaculum 11 Chlorobaculum tepidum 11 Genus: Chlorobium 10 Chlorobium tepidum 10 Genus: Chloroflexus 4 Chloroflexus aggregans 1 Chloroflexus aurantiacus 3 Genus: Chromobacterium 15 Chromobacterium violaceum 15 Genus: Chromohalobacter 1 Chromohalobacter salexigens 1 Genus: Clostridium 71 Clostridium acetobutylicum 27 Clostridium beijerinckii 1 Clostridium difficile 16 Clostridium leptum 2 Clostridium novyi 3 Clostridium perfringens 9 Clostridium phytofermentans 3 Clostridium symbiosum 3 Clostridium tetani 1 Clostridium thermocellum 6 Genus: Colwellia 7 Colwellia psychrerythraea 7 Genus: Corynebacterium 54 Corynebacterium diphtheriae 22 Corynebacterium glutamicum 32 Genus: Coxiella 1 Coxiella burnetii 1 Genus: Cupriavidus 1 Cupriavidus necator 1 Genus: Cytophaga 20 Cytophaga hutchinsonii 20 Genus: Deinococcus 20 Deinococcus geothermalis 3 Deinococcus radiodurans 17 Genus: Desulfitobacterium 13 Desulfitobacterium hafniense 13 Genus: Desulfotalea 2 Desulfotalea psychrophila 2 Genus: Desulfovibrio 18 Desulfovibrio desulfuricans 9 Desulfovibrio vulgaris 9 Genus: Desulfuromonas 1 Desulfuromonas acetoxidans 1 Genus: Enterococcus 60 Enterococcus faecalis 57 Enterococcus faecium 3 Genus: Escherichia 105 Escherichia coli 105 Genus: Eubacterium 15 Eubacterium eligens 3 Eubacterium rectale 9 Eubacterium ventriosum 3 Genus: Exiguobacterium 16 Exiguobacterium sibiricum 16 Genus: Fervidobacterium 1 Fervidobacterium nodosum 1 Genus: Frankia 1 Frankia sp. 1 Genus: Fulvimarina 1 Fulvimarina pelagi 1 Genus: Fusobacterium 2 Fusobacterium nucleatum 2 Genus: Geobacillus 14 Geobacillus kaustophilus 2 Geobacillus stearothermophilus 10 Geobacillus thermodenitrificans 2 Genus: Geobacter 22 Geobacter metallireducens 9 Geobacter sulfurreducens 13 Genus: Gloeobacter 1 Gloeobacter violaceus 1 Genus: Haemophilus 23 Haemophilus ducreyi 2 Haemophilus influenzae 13 Haemophilus somnus 8 Genus: Hahella 2 Hahella chejuensis 2 Genus: Haloarcula 6 Haloarcula marismortui 6 Genus: Halobacterium 1 Halobacterium sp. 1 Genus: Halorhodospira 1 Halorhodospira halophila 1 Genus: Helicobacter 15 Helicobacter pylori 15 Genus: Herpetosiphon 1 Herpetosiphon aurantiacus 1 Genus: Idiomarina 3 Idiomarina baltica 1 Idiomarina loihiensis 2 Genus: Jannaschia 13 Jannaschia 1 Jannaschia sp. 12 Genus: Klebsiella 20 Klebsiella pneumoniae 20 Genus: Lactobacillus 60 Lactobacillus acidophilus 9 Lactobacillus brevis 4 Lactobacillus casei 5 Lactobacillus delbrueckii 4 Lactobacillus plantarum 34 Lactobacillus reuteri 1 Lactobacillus salivarius 3 Genus: Lactococcus 4 Lactococcus lactis 4 Genus: Leeuwenhoekiella 1 Leeuwenhoekiella blandensis 1 Genus: Legionella 19 Legionella pneumophila 19 Genus: Listeria 56 Listeria innocua 26 Listeria monocytogenes 30 Genus: Magnetospirillum 5 Magnetospirillum magneticum 1 Magnetospirillum magnetotacticum 4 Genus: Mannheimia 1 Mannheimia succiniciproducens 1 Genus: Marinobacter 4 Marinobacter aquaeolei 4 Genus: Mesorhizobium 18 Mesorhizobium loti 16 Mesorhizobium sp. 2

Genus: Methanocaldococcus 26 Methanocaldococcus jannaschii 26 Genus: Methanococcus 12 Methanococcus jannaschii 2 Methanococcus maripaludis 10 Genus: Methanocorpusculum 1 Methanocorpusculum labreanum 1 Genus: Methanoculleus 2 Methanoculleus marisnigri 2 Genus: Methanopyrus 3 Methanopyrus kandleri 3 Genus: Methanosarcina 17 Methanosarcina mazei 17 Genus: Methanospirillum 2 Methanospirillum hungatei 2 Genus: Methanothermobacter 19 Methanothermobacter marburgensis 2 Methanothermobacter thermautotrophicus 17 Genus: Methylibium 2 Methylibium petroleiphilum 2 Genus: Methylobacillus 10 Methylobacillus flagellatus 10 Genus: Methylococcus 4 Methylococcus capsulatus 4 Genus: Moorella 1 Moorella thermoacetica 1 Genus: Mus 1 Mus musculus 1 Genus: Mycobacterium 18 Mycobacterium bovis 4 Mycobacterium smegmatis 1 Mycobacterium tuberculosis 12 Mycobacterium vanbaalenii 1 Genus: Myxococcus 1 Myxococcus xanthus 1 Genus: Neisseria 32 Neisseria gonorrhoeae 9 Neisseria meningitidis 23 Genus: Neptuniibacter 1 Neptuniibacter caesariensis 1 Genus: Nitrosomonas 27 Nitrosomonas europaea 27 Genus: Nitrosospira 4 Nitrosospira multiformis 4 Genus: Nocardia 1 Nocardia farcinica 1 Genus: Nostoc 31 Nostoc punctiforme 19 Nostoc sp. 12 Genus: Novosphingobium 22 Novosphingobium aromaticivorans 22 Genus: Oceanicola 1 Oceanicola granulosus 1 Genus: Oceanobacillus 6 Oceanobacillus iheyensis 6 Genus: Oenococcus 6 Oenococcus oeni 6 Genus: Oleispira 6 Oleispira antarctica 6 Genus: Parabacteroides 15 Parabacteroides distasonis 15 Genus: Paracoccus 1 Paracoccus denitrificans 1 Genus: Pectobacterium 17 Pectobacterium atrosepticum 16 Pectobacterium carotovorum 1 Genus: Pediococcus 2 Pediococcus pentosaceus 2 Genus: Picrophilus 1 Picrophilus torridus 1 Genus: Polaromonas 4 Polaromonas sp. 4 Genus: Porphyromonas 36 Porphyromonas gingivalis 36 Genus: Prevotella 1 Prevotella bryantii 1 Genus: Prochlorococcus 6 Prochlorococcus marinus 6 Genus: Pseudoalteromonas 2 Pseudoalteromonas atlantica 2 Genus: Pseudomonas 125 Pseudomonas aeruginosa 71 Pseudomonas fluorescens 11 Pseudomonas mendocina 1 Pseudomonas putida 13 Pseudomonas sp. 1 Pseudomonas syringae 28 Genus: Psychrobacter 6 Psychrobacter arcticus 6 Genus: Pyrococcus 27 Pyrococcus furiosus 13 Pyrococcus horikoshii 14 Genus: Ralstonia 30 Ralstonia eutropha 25 Ralstonia solanacearum 5 Genus: Rhodobacter 14 Rhodobacter sphaeroides 14 Genus: Rhodococcus 33 Rhodococcus jostii 4 Rhodococcus sp. 29 Genus: Rhodopirellula 2 Rhodopirellula baltica 2 Genus: Rhodopseudomonas 35 Rhodopseudomonas palustris 35 Genus: Rhodospirillum 13 Rhodospirillum rubrum 13 Genus: Roseovarius 7 Roseovarius nubinhibens 6 Roseovarius sp. 1 Genus: Rubrobacter 2 Rubrobacter xylanophilus 2 Genus: Ruegeria 9 Ruegeria pomeroyi 9 Genus: Ruminococcus 3 Ruminococcus gnavus 1 Ruminococcus obeum 2 Genus: Salinibacter 3 Salinibacter ruber 3 Genus: Salmonella 52 Salmonella choleraesuis 2 Salmonella enterica 5 Salmonella paratyphi 1 Salmonella typhi 2 Salmonella typhimurium 42 Genus: Shewanella 77 Shewanella amazonensis 8 Shewanella baltica 7 Shewanella denitrificans 6 Shewanella frigidimarina 6 Shewanella loihica 9 Shewanella oneidensis 37 Shewanella putrefaciens 4 Genus: Shigella 24 Shigella flexneri 24 Genus: Silicibacter 40 Silicibacter pomeroyi 32 Silicibacter sp. 8 Genus: Sinorhizobium 7 Sinorhizobium medicae 1 Sinorhizobium meliloti 6 Genus: Sphingomonas 1 Sphingomonas paucimobilis 1 Genus: Spirosoma 1 Spirosoma linguale 1 Genus: Staphylococcus 57 Staphylococcus aureus 33 Staphylococcus epidermidis 12 Staphylococcus haemolyticus 4 Staphylococcus saprophyticus 8 Genus: Streptococcus 97 Streptococcus agalactiae 12 Streptococcus mutans 16 Streptococcus pneumoniae 44 Streptococcus pyogenes 15 Streptococcus suis 3 Streptococcus thermophilus 7 Genus: Streptomyces 52 Streptomyces avermitilis 15 Streptomyces coelicolor 37 Genus: Sulfolobus 24 Sulfolobus solfataricus 24 Genus: Synechococcus 8 Synechococcus elongatus 6 Synechococcus sp. 2 Genus: Synechocystis 6 Synechocystis sp. 6 Genus: Syntrophomonas 2 Syntrophomonas wolfei 2 Genus: Syntrophus 4 Syntrophus aciditrophicus 4 Genus: Thermobifida 8 Thermobifida fusca 8 Genus: Thermococcus 1 Thermococcus kodakarensis 1 Genus: Thermoplasma 36 Thermoplasma acidophilum 30 Thermoplasma volcanium 6 Genus: Thermosynechococcus 2 Thermosynechococcus elongatus 2 Genus: Thermotoga 79 Thermotoga maritima 78 Thermotoga sp. 1 Genus: Thermus 4 Thermus thermophilus 4 Genus: Thiobacillus 3 Thiobacillus denitrificans 3 Genus: Treponema 1 Treponema denticola 1 Genus: Uncultured 6 Uncultured bacterium 5 Uncultured thermotogales 1 Genus: Ureaplasma 3 Ureaplasma parvum 3 Genus: Vibrio 84 Vibrio cholerae 30 Vibrio fischeri 7 Vibrio paracholerae 1 Vibrio parahaemolyticus 45 Vibrio splendidus 1 Genus: Vibrionales 1 Vibrionales bacterium 1 Genus: Wolinella 5 Wolinella succinogenes 5 Genus: Xanthomonas 18 Xanthomonas campestris 18 Genus: Xylella 5 Xylella fastidiosa 5 Genus: Yersinia 4 Yersinia enterocolitica 1 Yersinia pseudotuberculosis 3 Genus: Zymomonas 1 Zymomonas mobilis 1

Detailed PSI-2 structure counts for other organisms

Other Organisms Total	42
Artificial gene	2
Uncultured marine organism	6
Unidentified	11
Pseudomonas phage phi12	1
Staphylococcus phage 37	1
Sars coronavirus	12
Murid herpesvirus 4	2
Homo sapiens, bacteriophage t4	1
Homo sapiens, enterobacteria phage t4	1
Sars coronavirus tor2	1
Influenza a virus	1
Mengo virus	1
Vaccinia virus wr	1
Homo sapiens, enterobacteria phage t4, homo sapiens	1

IV. Novel Modeling Leverage

Calculations in this section updated March 1, 2010

Modeling leverage caculations are provided by Dr.Lukasz Jaroszewski affiliated with JCSG

Leverage provided by PSI-2 structures

Center	Total Leverage	Residue Leverage	Novel Leverage	Residue Leverage
LSC	1058498	259321521	218056	55255716
PSI-2	1272145	302356185	231200	59116183
PDB excluding PSI-2	3528980	1008622993	484770	186020919

V. Biological Theme Targets & Structures

Calculations in this section updated March 01, 2010

Biological Theme Targets by PSI Center

Center	Biomedical Targets	Metagenomics Targets	Community Nominated Targets
ATCG3D	7	0	0
CESG	931	0	440
CHTSB	125	0	0
ISFI	0	0	379
JCSG	19107	4266	3740
MCSG	3377	1500	1480
NESGC	7172	1142	640
NYCOMPS	0	0	458
NYSGXRC	1310	485	1480
Total	32029	7393	8616

Biomedical Targets & Structures by PSI Center

Center	Total Targets	Cloned Targets	Expressed Targets	Purified Targets	Crystallyzed Targets	NMR Targets	Targets In PDB	Structures In PDB
ATCG3D	7	7	7	7	6	0	6	8
CESG	931	723	667	159	25	3	8	7
CHTSB	125	124	29	10	0	0	1	17
JCSG	19107	18380	17724	17722	1643	0	624	665
MCSG	3377	3167	2218	1112	214	0	238	245
NESGC	7172	1406	1366	422	110	61	95	100
NYSGXRC	1310	987	892	457	102	0	66	73
Total	32029	24794	22903	19889	2100	64	1038	1115

Metagenomic Targets & Structures by PSI Center

Center	Total Targets	Cloned Targets	Expressed Targets	Purified Targets	Crystallyzed Targets	NMR Targets	Targets In PDB	Structures In PDB
JCSG	4266	4136	4134	4134	321	0	72	72
MCSG	1500	1430	859	306	64	0	63	63
NESGC	1142	775	772	258	62	18	39	43
NYSGXRC	485	451	396	207	52	0	30	33
Total	7393	6792	6161	4905	499	18	204	211

Community Nominated Targets & Structures by PSI Center

Center	Total Targets	Cloned Targets	Expressed Targets	Purified Targets	Crystallyzed Targets	NMR Targets	Targets In PDB	Structures In PDB
CESG	440	311	240	69	36	12	29	36
ISFI	379	293	200	137	95	0	35	14
JCSG	3740	3615	3613	3613	280	0	70	71
MCSG	1480	1382	1068	540	98	0	35	36
NESGC	640	336	322	198	79	29	64	77
NYCOMPS	458	445	83	43	0	0	0	0
NYSGXRC	1480	1055	883	439	147	0	102	137
Total	8616	7436	6409	5039	735	41	335	371

VI. PSI PFAM Domain Family Coverage

Calculations in this section updated February 1, 2010

Number of PFAM families for which PSI provided the first structure representative

Total PFAM Families	Total PFAM Families in PDB	PSI-1 PFAM Families	PSI-2 PFAM Families
11912	5268	347	519