Metrics Describing Progress of the Protein Structure Initiative
Updated December 01, 2011
I. Progress of the PSI
II. Number of Experimental Structures and Residues
III. Impact and Classification of Structures
IV. Novel Modeling Leverage
V. Biological Theme Targets & Structures
VI. PSI 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, PSI-2, PSI-3)
- 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 12-01-2011
- PSI-3: The PSI:Biology program of the protein structure initiative (PSI) (07-01-2010 - ongoing). Statistics on this page reflect PSI-3 data deposited after 07-01-2010 and released before 12-01-2011
- LSC: are the four Protein Structure Initiative (PSI) large-scale production centers; namely MCSG, JCSG, NESG, and NYSGXRC/NYSGRC
- 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 |
390 |
427 |
| PSI-2 grant year 2006 |
620 |
700 |
| PSI-2 grant year 2007 |
682 |
718 |
| PSI-2 grant year 2008 |
796 |
818 |
| PSI-2 grant year 2009 |
822 |
879 |
| PSI-2 grant extension |
217 |
244 |
| PSI-2 total depositions |
3527 |
3786 |
| PSI-3 grant year 2010 |
280 |
283 |
| PSI-3 total depositions |
377 |
381 |
| PSI-1 + PSI-2 + PSI-3 |
4804 |
5583 |
PSI-2 grant year 2005:
PSI-2 structures deposited between July 1, 2005 and July 1, 2006
PSI-2 grant year 2006:
PSI-2 structures deposited between July 1, 2006 and July 1, 2007
PSI-2 grant year 2007:
PSI-2 structures deposited between July 1, 2007 and July 1, 2008
PSI-2 grant year 2008:
PSI-2 structures deposited between July 1, 2008 and July 1, 2009
PSI-2 grant year 2009:
PSI-2 structures deposited between July 1, 2009 and July 1, 2010
PSI-2 grant extension:
PSI-2 structures deposited between July 1, 2010 and December 01, 2011
PSI-2 total depositions:
PSI-2 structures deposited between July 1, 2005 and December 01, 2011
PSI-3 grant year 2010:
PSI-3 structures deposited between July 1, 2010 and July 1, 2011
PSI-3 total depositions:
PSI-3 structures deposited between July 1, 2010 and December 01, 2011
PSI-1 + PSI-2 + PSI-3:
All PSI structures released before December 01, 2011
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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 96 PSI-derived structures deposited as of September 1, 2001.
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II. Number of Experimental Structures and Residues
Structures determined in PSI-1
| Center |
Total Structures |
Distinct Structures |
Distinct Residues |
Novel Structures |
Novel Residues |
| LSC |
898 |
792 |
180109 |
453 |
99731 |
| ALL-PSI-1 |
1416 |
1157 |
265929 |
622 |
137025 |
| ALL PDB |
19865 |
7111 |
1704005 |
2735 |
645949 |
Calculations in this table are based on PDB data deposited before July 1, 2005.
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Structures determined in PSI-2
| Center |
Total Structures |
Distinct Structures |
Distinct Residues |
Novel Structures |
Novel Residues |
| LSC |
3527 |
3166 |
719603 |
1957 |
441959 |
| ALL-PSI-2 |
3786 |
3271 |
744587 |
2018 |
456021 |
| ALL PDB |
43100 |
15604 |
3975602 |
5922 |
1435827 |
Calculations in this table are based on PDB data deposited after July 1, 2005 and released before December 01, 2011.
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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 December 01, 2011.
Classification of PSI-2 structures
| Center |
Total Structures |
X-ray |
NMR |
Membrane Proteins |
Eukaryotes |
Human |
Other |
Prokaryotes |
| LSC |
3527 |
3159 |
368 |
24 |
185 |
100 |
46 |
3274 |
| ALL-PSI-2 |
3786 |
3380 |
406 |
81 |
345 |
147 |
58 |
3360 |
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Classification of PSI-2 structures by organism
| Eukaryotes Total | 345 |
| Prokaryotes Total | 3360 |
| Other Organisms Total | 58 |
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Detailed PSI-2 structure counts for eukaryotes
| Eukaryotes Total | 345 |
| Aequorea victoria | 1 |
| Anopheles gambiae | 2 |
| Antirrhinum majus | 1 |
| Arabidopsis thaliana | 59 |
| Ashbya gossypii | 2 |
| Aspergillus fumigatus | 1 |
| Aspergillus oryzae | 2 |
| Babesia bovis | 1 |
| Bos taurus | 3 |
| Brugia malayi | 1 |
| Caenorhabditis elegans | 11 |
| Candida albicans | 1 |
| Candida glabrata | 1 |
| Coccidioides immitis | 1 |
| Cyanidioschyzon merolae | 1 |
| Danio rerio | 7 |
| Drosophila melanogaster | 3 |
| Encephalitozoon cuniculi | 4 |
| Engyodontium album | 1 |
| Galdieria sulphuraria | 7 |
| Gibberella zeae | 2 |
| Homo sapiens | 147 |
| Mus musculus | 35 |
| Oncorhynchus mykiss | 1 |
| Oryza sativa | 1 |
| Pentadiplandra brazzeana | 1 |
| Pichia guilliermondii | 1 |
| Rana pipiens | 2 |
| Rattus norvegicus | 5 |
| Saccharomyces cerevisiae | 30 |
| Schizosaccharomyces pombe | 2 |
| Solanum lycopersicum | 1 |
| Spinacia oleracea | 1 |
| Sus scrofa | 1 |
| Toxoplasma gondii | 3 |
| Trypanosoma brucei | 1 |
| Xenopus laevis | 1 |
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Detailed PSI-2 structure counts for prokaryotes
| Prokaryotes Total |
3360 |
| Genus: Acidithiobacillus | 5 | | Acidithiobacillus ferrooxidans | 5 |
| Genus: Acidothermus | 1 | | Acidothermus cellulolyticus | 1 |
| Genus: Acinetobacter | 9 | | Acinetobacter baumannii | 1 |
| Acinetobacter calcoaceticus | 1 |
| Acinetobacter sp. | 7 |
| Genus: Actinobacillus | 3 | | Actinobacillus succinogenes | 3 |
| Genus: Aeromonas | 4 | | Aeromonas hydrophila | 1 |
| Aeromonas salmonicida | 3 |
| Genus: Aeropyrum | 5 | | Aeropyrum pernix | 5 |
| Genus: Agrobacterium | 96 | | Agrobacterium tumefaciens | 95 |
| Agrobacterium vitis | 1 |
| Genus: Alcanivorax | 2 | | Alcanivorax borkumensis | 2 |
| Genus: Alicyclobacillus | 1 | | Alicyclobacillus acidocaldarius | 1 |
| 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 | 9 | | Aquifex aeolicus | 9 |
| Genus: Archaeoglobus | 59 | | Archaeoglobus fulgidus | 59 |
| Genus: Arthrobacter | 11 | | Arthrobacter aurescens | 5 |
| Arthrobacter sp. | 6 |
| Genus: Azoarcus | 1 | | Azoarcus sp. | 1 |
| Genus: Azorhizobium | 1 | | Azorhizobium caulinodans | 1 |
| Genus: Azotobacter | 2 | | Azotobacter vinelandii | 2 |
| Genus: Bacillus | 266 | | Bacillus anthracis | 15 |
| Bacillus cereus | 53 |
| Bacillus clausii | 2 |
| Bacillus cytotoxicus | 1 |
| Bacillus halodurans | 55 |
| Bacillus licheniformis | 2 |
| Bacillus subtilis | 127 |
| Bacillus thuringiensis | 11 |
| Genus: Bacteroides | 205 | | Bacteroides caccae | 1 |
| Bacteroides fragilis | 56 |
| Bacteroides ovatus | 9 |
| Bacteroides thetaiotaomicron | 107 |
| Bacteroides uniformis | 1 |
| Bacteroides vulgatus | 31 |
| Genus: Bartonella | 7 | | Bartonella henselae | 7 |
| Genus: Bdellovibrio | 2 | | Bdellovibrio bacteriovorus | 2 |
| Genus: Bermanella | 1 | | Bermanella marisrubri | 1 |
| Genus: Bifidobacterium | 12 | | Bifidobacterium adolescentis | 7 |
| Bifidobacterium longum | 5 |
| Genus: Blastochloris | 1 | | Blastochloris viridis | 1 |
| Genus: Bordetella | 47 | | Bordetella bronchiseptica | 20 |
| Bordetella parapertussis | 16 |
| Bordetella pertussis | 11 |
| Genus: Borrelia | 1 | | Borrelia burgdorferi | 1 |
| Genus: Bradyrhizobium | 3 | | Bradyrhizobium japonicum | 3 |
| Genus: Burkholderia | 37 | | Burkholderia mallei | 4 |
| Burkholderia phymatum | 1 |
| Burkholderia phytofirmans | 2 |
| Burkholderia pseudomallei | 4 |
| Burkholderia sp. | 1 |
| Burkholderia thailandensis | 7 |
| Burkholderia xenovorans | 18 |
| Genus: Caldicellulosiruptor | 1 | | Caldicellulosiruptor saccharolyticus | 1 |
| Genus: Campylobacter | 11 | | Campylobacter jejuni | 11 |
| Genus: Carboxydothermus | 2 | | Carboxydothermus hydrogenoformans | 2 |
| Genus: Caulobacter | 13 | | Caulobacter crescentus | 7 |
| Caulobacter vibrioides | 6 |
| Genus: Chlamydia | 1 | | Chlamydia trachomatis | 1 |
| Genus: Chlamydophila | 1 | | Chlamydophila abortus | 1 |
| Genus: Chlorobaculum | 13 | | Chlorobaculum tepidum | 13 |
| Genus: Chlorobium | 10 | | Chlorobium tepidum | 10 |
| Genus: Chloroflexus | 5 | | Chloroflexus aggregans | 1 |
| Chloroflexus aurantiacus | 4 |
| Genus: Chromobacterium | 23 | | Chromobacterium violaceum | 23 |
| Genus: Chromohalobacter | 4 | | Chromohalobacter salexigens | 4 |
| Genus: Clostridium | 84 | | Clostridium acetobutylicum | 31 |
| Clostridium beijerinckii | 1 |
| Clostridium difficile | 19 |
| Clostridium leptum | 3 |
| Clostridium novyi | 3 |
| Clostridium perfringens | 12 |
| Clostridium phytofermentans | 3 |
| Clostridium symbiosum | 3 |
| Clostridium tetani | 1 |
| Clostridium thermocellum | 8 |
| Genus: Colwellia | 10 | | Colwellia psychrerythraea | 10 |
| Genus: Corynebacterium | 64 | | Corynebacterium diphtheriae | 24 |
| Corynebacterium glutamicum | 40 |
| Genus: Coxiella | 1 | | Coxiella burnetii | 1 |
| Genus: Cupriavidus | 2 | | Cupriavidus metallidurans | 1 |
| Cupriavidus necator | 1 |
| Genus: Cytophaga | 25 | | Cytophaga hutchinsonii | 25 |
| Genus: Deinococcus | 22 | | Deinococcus geothermalis | 3 |
| Deinococcus radiodurans | 19 |
| Genus: Desulfitobacterium | 20 | | Desulfitobacterium hafniense | 20 |
| Genus: Desulfotalea | 2 | | Desulfotalea psychrophila | 2 |
| Genus: Desulfovibrio | 21 | | Desulfovibrio desulfuricans | 9 |
| Desulfovibrio vulgaris | 12 |
| Genus: Desulfuromonas | 1 | | Desulfuromonas acetoxidans | 1 |
| Genus: Dyadobacter | 1 | | Dyadobacter fermentans | 1 |
| Genus: Enterococcus | 65 | | Enterococcus faecalis | 62 |
| Enterococcus faecium | 3 |
| Genus: Erwinia | 2 | | Erwinia carotovora | 2 |
| Genus: Escherichia | 120 | | Escherichia coli | 120 |
| Genus: Eubacterium | 13 | | Eubacterium eligens | 3 |
| Eubacterium rectale | 6 |
| Eubacterium ventriosum | 4 |
| Genus: Exiguobacterium | 17 | | Exiguobacterium sibiricum | 17 |
| Genus: Fervidobacterium | 1 | | Fervidobacterium nodosum | 1 |
| Genus: Frankia | 1 | | Frankia sp. | 1 |
| Genus: Fulvimarina | 1 | | Fulvimarina pelagi | 1 |
| Genus: Fusobacterium | 4 | | Fusobacterium nucleatum | 4 |
| Genus: Geobacillus | 17 | | Geobacillus kaustophilus | 2 |
| Geobacillus sp. | 3 |
| Geobacillus stearothermophilus | 10 |
| Geobacillus thermodenitrificans | 2 |
| Genus: Geobacter | 28 | | Geobacter metallireducens | 11 |
| Geobacter sulfurreducens | 17 |
| Genus: Gloeobacter | 1 | | Gloeobacter violaceus | 1 |
| Genus: Haemophilus | 39 | | Haemophilus ducreyi | 3 |
| Haemophilus influenzae | 28 |
| Haemophilus somnus | 8 |
| Genus: Hahella | 2 | | Hahella chejuensis | 2 |
| Genus: Haloarcula | 7 | | Haloarcula marismortui | 7 |
| Genus: Halobacterium | 1 | | Halobacterium sp. | 1 |
| Genus: Halorhodospira | 1 | | Halorhodospira halophila | 1 |
| Genus: Helicobacter | 20 | | Helicobacter pylori | 20 |
| Genus: Herpetosiphon | 1 | | Herpetosiphon aurantiacus | 1 |
| Genus: Idiomarina | 3 | | Idiomarina baltica | 1 |
| Idiomarina loihiensis | 2 |
| Genus: Jannaschia | 14 | | Jannaschia | 1 |
| Jannaschia sp. | 13 |
| Genus: Jonesia | 1 | | Jonesia denitrificans | 1 |
| Genus: Klebsiella | 27 | | Klebsiella pneumoniae | 26 |
| Klebsiella variicola | 1 |
| Genus: Kosmotoga | 1 | | Kosmotoga olearia | 1 |
| Genus: Lactobacillus | 70 | | Lactobacillus acidophilus | 11 |
| Lactobacillus brevis | 10 |
| Lactobacillus casei | 5 |
| Lactobacillus delbrueckii | 4 |
| Lactobacillus plantarum | 36 |
| Lactobacillus reuteri | 1 |
| Lactobacillus salivarius | 3 |
| Genus: Lactococcus | 6 | | Lactococcus lactis | 6 |
| Genus: Leeuwenhoekiella | 1 | | Leeuwenhoekiella blandensis | 1 |
| Genus: Legionella | 25 | | Legionella pneumophila | 25 |
| Genus: Leptospirillum | 5 | | Leptospirillum rubarum | 5 |
| Genus: Listeria | 71 | | Listeria innocua | 36 |
| Listeria monocytogenes | 35 |
| Genus: Magnetospirillum | 5 | | Magnetospirillum magneticum | 1 |
| Magnetospirillum magnetotacticum | 4 |
| Genus: Mannheimia | 1 | | Mannheimia succiniciproducens | 1 |
| Genus: Marine | 2 | | Marine actinobacterium | 2 |
| Genus: Marinobacter | 8 | | Marinobacter aquaeolei | 8 |
|
| Genus: Mesorhizobium | 20 | | Mesorhizobium loti | 18 |
| Mesorhizobium sp. | 2 |
| Genus: Methanocaldococcus | 28 | | Methanocaldococcus jannaschii | 28 |
| 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 | 22 | | Methanosarcina acetivorans | 2 |
| Methanosarcina mazei | 20 |
| Genus: Methanospirillum | 2 | | Methanospirillum hungatei | 2 |
| Genus: Methanothermobacter | 18 | | Methanothermobacter marburgensis | 2 |
| Methanothermobacter thermautotrophicus | 16 |
| Genus: Methylibium | 2 | | Methylibium petroleiphilum | 2 |
| Genus: Methylobacillus | 12 | | Methylobacillus flagellatus | 12 |
| Genus: Methylococcus | 5 | | Methylococcus capsulatus | 5 |
| Genus: Micromonospora | 7 | | Micromonospora echinospora | 7 |
| Genus: Moorella | 1 | | Moorella thermoacetica | 1 |
| Genus: Mycobacterium | 22 | | Mycobacterium bovis | 4 |
| Mycobacterium smegmatis | 3 |
| Mycobacterium tuberculosis | 14 |
| Mycobacterium vanbaalenii | 1 |
| Genus: Mycoplasma | 2 | | Mycoplasma synoviae | 2 |
| Genus: Myxococcus | 2 | | Myxococcus xanthus | 2 |
| Genus: Neisseria | 36 | | Neisseria gonorrhoeae | 9 |
| Neisseria meningitidis | 27 |
| Genus: Neptuniibacter | 1 | | Neptuniibacter caesariensis | 1 |
| Genus: Nitrosomonas | 28 | | Nitrosomonas europaea | 28 |
| Genus: Nitrosospira | 5 | | Nitrosospira multiformis | 5 |
| Genus: Nocardia | 1 | | Nocardia farcinica | 1 |
| Genus: Nostoc | 36 | | Nostoc punctiforme | 20 |
| Nostoc sp. | 16 |
| Genus: Novosphingobium | 23 | | Novosphingobium aromaticivorans | 23 |
| Genus: Oceanicola | 1 | | Oceanicola granulosus | 1 |
| Genus: Oceanobacillus | 6 | | Oceanobacillus iheyensis | 6 |
| Genus: Oenococcus | 7 | | Oenococcus oeni | 7 |
| Genus: Oleispira | 8 | | Oleispira antarctica | 8 |
| Genus: Parabacteroides | 23 | | Parabacteroides distasonis | 23 |
| Genus: Paracoccus | 2 | | Paracoccus denitrificans | 2 |
| Genus: Pectobacterium | 18 | | Pectobacterium atrosepticum | 17 |
| Pectobacterium carotovorum | 1 |
| Genus: Pediococcus | 5 | | Pediococcus pentosaceus | 5 |
| Genus: Pelobacter | 1 | | Pelobacter carbinolicus | 1 |
| Genus: Picrophilus | 1 | | Picrophilus torridus | 1 |
| Genus: Polaromonas | 4 | | Polaromonas sp. | 4 |
| Genus: Porphyromonas | 38 | | Porphyromonas gingivalis | 38 |
| Genus: Prevotella | 1 | | Prevotella bryantii | 1 |
| Genus: Prochlorococcus | 6 | | Prochlorococcus marinus | 6 |
| Genus: Proteus | 1 | | Proteus mirabilis | 1 |
| Genus: Pseudoalteromonas | 2 | | Pseudoalteromonas atlantica | 2 |
| Genus: Pseudomonas | 163 | | Pseudomonas aeruginosa | 86 |
| Pseudomonas fluorescens | 20 |
| Pseudomonas mendocina | 1 |
| Pseudomonas putida | 18 |
| Pseudomonas sp. | 1 |
| Pseudomonas syringae | 37 |
| Genus: Pseudovibrio | 2 | | Pseudovibrio sp. | 2 |
| Genus: Psychrobacter | 6 | | Psychrobacter arcticus | 6 |
| Genus: Pyrococcus | 30 | | Pyrococcus furiosus | 15 |
| Pyrococcus horikoshii | 15 |
| Genus: Ralstonia | 32 | | Ralstonia eutropha | 26 |
| Ralstonia pickettii | 1 |
| Ralstonia solanacearum | 5 |
| Genus: Rhizobium | 4 | | Rhizobium etli | 2 |
| Rhizobium leguminosarum | 2 |
| Genus: Rhodobacter | 24 | | Rhodobacter capsulatus | 3 |
| Rhodobacter sphaeroides | 21 |
| Genus: Rhodococcus | 34 | | Rhodococcus | 1 |
| Rhodococcus jostii | 5 |
| Rhodococcus sp. | 28 |
| Genus: Rhodopirellula | 2 | | Rhodopirellula baltica | 2 |
| Genus: Rhodopseudomonas | 45 | | Rhodopseudomonas palustris | 45 |
| Genus: Rhodospirillum | 14 | | Rhodospirillum rubrum | 14 |
| Genus: Roseovarius | 7 | | Roseovarius nubinhibens | 6 |
| Roseovarius sp. | 1 |
| Genus: Rubrobacter | 2 | | Rubrobacter xylanophilus | 2 |
| Genus: Ruegeria | 14 | | Ruegeria pomeroyi | 11 |
| Ruegeria sp. | 3 |
| Genus: Ruminococcus | 12 | | Ruminococcus gnavus | 3 |
| Ruminococcus obeum | 9 |
| Genus: Salinibacter | 4 | | Salinibacter ruber | 4 |
| Genus: Salmonella | 45 | | Salmonella enterica | 10 |
| Salmonella paratyphi | 1 |
| Salmonella typhimurium | 34 |
| Genus: Shewanella | 94 | | Shewanella amazonensis | 10 |
| Shewanella baltica | 8 |
| Shewanella denitrificans | 7 |
| Shewanella frigidimarina | 8 |
| Shewanella loihica | 9 |
| Shewanella oneidensis | 46 |
| Shewanella pealeana | 1 |
| Shewanella putrefaciens | 4 |
| Shewanella sp. | 1 |
| Genus: Shigella | 31 | | Shigella flexneri | 31 |
| Genus: Silicibacter | 41 | | Silicibacter pomeroyi | 33 |
| Silicibacter sp. | 8 |
| Genus: Sinorhizobium | 11 | | Sinorhizobium medicae | 1 |
| Sinorhizobium meliloti | 10 |
| Genus: Sphingomonas | 1 | | Sphingomonas paucimobilis | 1 |
| Genus: Spirosoma | 1 | | Spirosoma linguale | 1 |
| Genus: Staphylococcus | 64 | | Staphylococcus aureus | 37 |
| Staphylococcus epidermidis | 14 |
| Staphylococcus haemolyticus | 4 |
| Staphylococcus saprophyticus | 9 |
| Genus: Streptococcus | 110 | | Streptococcus agalactiae | 15 |
| Streptococcus mutans | 19 |
| Streptococcus pneumoniae | 47 |
| Streptococcus pyogenes | 16 |
| Streptococcus suis | 3 |
| Streptococcus thermophilus | 10 |
| Genus: Streptomyces | 57 | | Streptomyces avermitilis | 19 |
| Streptomyces coelicolor | 38 |
| Genus: Sulfolobus | 27 | | Sulfolobus solfataricus | 27 |
| Genus: Sulfurospirillum | 1 | | Sulfurospirillum deleyianum | 1 |
| Genus: Synechococcus | 9 | | Synechococcus elongatus | 7 |
| Synechococcus sp. | 2 |
| Genus: Synechocystis | 13 | | Synechocystis | 1 |
| Synechocystis sp. | 12 |
| Genus: Syntrophomonas | 3 | | Syntrophomonas wolfei | 3 |
| Genus: Syntrophus | 4 | | Syntrophus aciditrophicus | 4 |
| Genus: Thermobifida | 10 | | Thermobifida fusca | 10 |
| Genus: Thermococcus | 1 | | Thermococcus kodakarensis | 1 |
| Genus: Thermoplasma | 38 | | Thermoplasma acidophilum | 30 |
| Thermoplasma volcanium | 8 |
| Genus: Thermosynechococcus | 2 | | Thermosynechococcus elongatus | 2 |
| Genus: Thermotoga | 90 | | Thermotoga maritima | 89 |
| Thermotoga sp. | 1 |
| Genus: Thermus | 4 | | Thermus thermophilus | 4 |
| Genus: Thiobacillus | 4 | | Thiobacillus denitrificans | 4 |
| Genus: Treponema | 1 | | Treponema denticola | 1 |
| Genus: Uncultured | 6 | | Uncultured bacterium | 5 |
| Uncultured thermotogales | 1 |
| Genus: Ureaplasma | 3 | | Ureaplasma parvum | 3 |
| Genus: Vibrio | 101 | | Vibrio cholerae | 38 |
| Vibrio fischeri | 10 |
| Vibrio paracholerae | 1 |
| Vibrio parahaemolyticus | 51 |
| Vibrio splendidus | 1 |
| Genus: Vibrionales | 1 | | Vibrionales bacterium | 1 |
| Genus: Wolinella | 7 | | Wolinella succinogenes | 7 |
| Genus: Xanthomonas | 18 | | Xanthomonas campestris | 18 |
| Genus: Xylella | 7 | | Xylella fastidiosa | 7 |
| Genus: Yersinia | 8 | | Yersinia enterocolitica | 2 |
| Yersinia pestis | 1 |
| Yersinia pseudotuberculosis | 5 |
| Genus: Zymomonas | 1 | | Zymomonas mobilis | 1 |
|
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Detailed PSI-2 structure counts for other organisms
| Other Organisms Total | 58 |
| Chimera | 1 |
| Rattus norvegicus, saccharomyces cerevisiae | 1 |
| Unknown | 21 |
| Artificial gene | 4 |
| Uncultured marine organism | 6 |
| Unidentified | 11 |
| Virus | 36 |
| Bacteriophage p1 | 1 |
| Homo sapiens, bacteriophage t4 | 1 |
| Homo sapiens, enterobacteria phage t4 | 9 |
| Homo sapiens, enterobacteria phage t4, homo sapiens | 1 |
| Influenza a virus | 2 |
| Mengo virus | 1 |
| Moloney murine leukemia virus | 1 |
| Murid herpesvirus 4 | 2 |
| Pseudomonas phage luz7 | 1 |
| Pseudomonas phage phi12 | 1 |
| Pseudomonas phage yua | 1 |
| Sars coronavirus | 13 |
| Staphylococcus phage | 1 |
| Vaccinia virus wr | 1 |
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IV. Novel Modeling Leverage
Calculations in this section updated October 5, 2011
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 |
1233729 |
304119628 |
250016 |
64765245 |
| PSI-2 |
1462817 |
352173350 |
266758 |
69997509 |
| PDB excluding PSI-2 |
3828929 |
1115315109 |
635537 |
241783799 |
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V. Biological Theme Targets & Structures
Calculations in this section updated December 01, 2011
Biological Theme Targets by PSI Center
| Center |
Biomedical Targets |
Metagenomics Targets |
Community Nominated Targets |
| ATCG3D |
7 |
0 |
0 |
| CESG |
983 |
0 |
442 |
| CHTSB |
129 |
0 |
0 |
| GPCR |
0 |
0 |
3 |
| ISFI |
0 |
0 |
428 |
| JCSG |
21843 |
2436 |
2078 |
| MCSG |
4318 |
1500 |
1945 |
| MPP |
232 |
0 |
284 |
| NESG |
8561 |
1847 |
811 |
| NYCOMPS |
0 |
0 |
532 |
| NYSGRC |
9593 |
0 |
302 |
| NYSGXRC |
1335 |
485 |
1489 |
| TMPC |
48 |
0 |
49 |
| Total |
54744 |
6268 |
11410 |
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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 |
983 |
770 |
689 |
173 |
32 |
3 |
10 |
8 |
| CHTSB |
129 |
124 |
29 |
10 |
0 |
0 |
5 |
21 |
| JCSG |
21843 |
21108 |
12469 |
12467 |
1857 |
0 |
738 |
798 |
| MCSG |
4318 |
3515 |
2595 |
1265 |
287 |
0 |
276 |
304 |
| MPP |
232 |
51 |
47 |
5 |
0 |
0 |
0 |
0 |
| NESG |
8561 |
2578 |
2418 |
736 |
50 |
89 |
129 |
141 |
| NYSGRC |
9593 |
2089 |
1794 |
481 |
51 |
0 |
41 |
43 |
| NYSGXRC |
1335 |
1010 |
911 |
462 |
107 |
0 |
69 |
77 |
| TMPC |
48 |
32 |
26 |
10 |
0 |
0 |
0 |
0 |
| Total |
54744 |
35893 |
24306 |
16833 |
2390 |
92 |
1274 |
1711 |
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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 |
2436 |
2348 |
1625 |
1625 |
387 |
0 |
113 |
116 |
| MCSG |
1500 |
1430 |
860 |
323 |
70 |
0 |
64 |
71 |
| NESG |
1847 |
1127 |
1123 |
409 |
45 |
28 |
67 |
77 |
| NYSGXRC |
485 |
451 |
396 |
207 |
52 |
0 |
31 |
35 |
| Total |
6268 |
5356 |
4004 |
2564 |
554 |
28 |
275 |
299 |
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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 |
442 |
313 |
243 |
81 |
39 |
12 |
30 |
40 |
| GPCR |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
| ISFI |
428 |
330 |
244 |
210 |
175 |
0 |
129 |
13 |
| JCSG |
2078 |
1992 |
1573 |
1573 |
363 |
0 |
111 |
113 |
| MCSG |
1945 |
1614 |
1304 |
581 |
128 |
0 |
49 |
50 |
| MPP |
284 |
180 |
165 |
28 |
0 |
0 |
0 |
0 |
| NESG |
811 |
564 |
523 |
292 |
49 |
38 |
83 |
97 |
| NYCOMPS |
532 |
362 |
90 |
43 |
0 |
0 |
0 |
0 |
| NYSGRC |
302 |
302 |
297 |
56 |
17 |
0 |
11 |
14 |
| NYSGXRC |
1489 |
1288 |
1066 |
514 |
174 |
0 |
128 |
178 |
| TMPC |
49 |
41 |
27 |
8 |
0 |
0 |
0 |
0 |
| Total |
11410 |
8555 |
6572 |
3808 |
945 |
50 |
541 |
589 |
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VI. PSI PFAM Domain Family Coverage
Calculations in this section updated October 5, 2011
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 |
| 12273 |
5564 |
355 |
561 |
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