Validation
Control set
Proteins whose function is already well known. We run them through the same model as the dark proteins and compare its answer with established biology. This set will grow into a benchmark of 50–100 known proteins.
5control proteins
79correct items
11missed
12speculative
77%of 102 items correct
Correct matches known biology · Missed known function not mentioned · Speculative predicted without established evidence
ADRB2 Beta-2 adrenergic receptor
P07550
26 correct · 2 missed · 8 speculativeProtein page →
72%correct26 correct · 2 missed · 8 speculative
CorrectMissedSpeculative
Known biology
- protein-containing complex binding · GO:0044877Correct
- amyloid-beta binding · GO:0001540Correct
- potassium channel regulator activity · GO:0015459Correct
- protein homodimerization activity · GO:0042803Correct
- amyloid-beta binding · GO:0001540Correct
- beta2-adrenergic receptor activity · GO:0004941Correct
- response to psychosocial stress · GO:1990911Correct
- cell surface receptor signaling pathway · GO:0007166Correct
- adrenergic receptor signaling pathway · GO:0071875Correct
- negative regulation of G protein-coupled receptor signaling pathway · GO:0045744Correct
- positive regulation of autophagosome maturation · GO:1901098Correct
- adenylate cyclase-modulating G protein-coupled receptor signaling pathway · GO:0007188Correct
- positive regulation of autophagosome maturation · GO:1901098Correct
- endosome to lysosome transport · GO:0008333Correct
- cell surface receptor signaling pathway · GO:0007166Correct
- positive regulation of MAPK cascade · GO:0043410Correct
- positive regulation of autophagosome maturation · GO:1901098Correct
- negative regulation of G protein-coupled receptor signaling pathway · GO:0045744Correct
- cellular response to amyloid-beta · GO:1904646Correct
- receptor-mediated endocytosis · GO:0006898Correct
- signaling receptor complex · GO:0043235Correct
- Golgi apparatus · GO:0005794Correct
- plasma membrane · GO:0005886Correct
- endosome membrane · GO:0010008Correct
- lysosome · GO:0005764Correct
- clathrin-coated endocytic vesicle membrane · GO:0030669Correct
- norepinephrine binding · GO:0051380Missed
- positive regulation of glutamate receptor signaling pathway · GO:1900451Missed
Source: UniProt P07550, GO annotations (all evidence for "correct"; experimental evidence for "missed", max 2 per aspect shown)
AI prediction
- GO:0044877 protein-containing complex bindingCorrect
- GO:0042277 peptide bindingCorrect
- GO:0015459 potassium channel regulator activityCorrect
- GO:0042803 protein homodimerization activityCorrect
- GO:0001540 amyloid-beta bindingCorrect
- GO:0004935 adrenergic receptor activityCorrect
- GO:0006950 response to stressCorrect
- GO:0007166 cell surface receptor signaling pathwayCorrect
- GO:0071875 adrenergic receptor signaling pathwayCorrect
- GO:0045744 negative regulation of G protein-coupled receptor signaling pathwayCorrect
- GO:0010508 positive regulation of autophagyCorrect
- GO:0007188 adenylate cyclase-modulating G protein-coupled receptor signaling pathwayCorrect
- GO:2000273 positive regulation of signaling receptor activitySpeculative
- GO:0043243 positive regulation of protein-containing complex disassemblyCorrect
- GO:0065003 protein-containing complex assemblySpeculative
- GO:0010738 regulation of protein kinase A signalingSpeculative
- GO:0008333 endosome to lysosome transportCorrect
- GO:0007169 transmembrane receptor protein tyrosine kinase signaling pathwayCorrect
- GO:0043410 positive regulation of MAPK cascadeCorrect
- GO:2000311 regulation of AMPA receptor activitySpeculative
- GO:1901098 positive regulation of autophagosome maturationCorrect
- GO:0002029 desensitization of G protein-coupled receptor signaling pathwayCorrect
- GO:0032091 negative regulation of protein bindingSpeculative
- GO:1904646 cellular response to amyloid-betaCorrect
- GO:0006898 receptor-mediated endocytosisCorrect
- GO:0007190 activation of adenylate cyclase activitySpeculative
- GO:1901653 cellular response to peptideSpeculative
- GO:2000479 regulation of cAMP-dependent protein kinase activitySpeculative
- GO:0043235 receptor complexCorrect
- GO:0005794 Golgi apparatusCorrect
- GO:0005886 plasma membraneCorrect
- GO:0010008 endosome membraneCorrect
- GO:0005764 lysosomeCorrect
- GO:0030669 clathrin-coated endocytic vesicle membraneCorrect
BioReason-Pro
Item by item
| Aspect | Known biology | AI prediction | Verdict |
|---|---|---|---|
| Molecular function | protein-containing complex binding · GO:0044877 | GO:0044877 protein-containing complex binding | Correct |
| Molecular function | amyloid-beta binding · GO:0001540 | GO:0042277 peptide binding | Correct |
| Molecular function | potassium channel regulator activity · GO:0015459 | GO:0015459 potassium channel regulator activity | Correct |
| Molecular function | protein homodimerization activity · GO:0042803 | GO:0042803 protein homodimerization activity | Correct |
| Molecular function | amyloid-beta binding · GO:0001540 | GO:0001540 amyloid-beta binding | Correct |
| Molecular function | beta2-adrenergic receptor activity · GO:0004941 | GO:0004935 adrenergic receptor activity | Correct |
| Biological process | response to psychosocial stress · GO:1990911 | GO:0006950 response to stress | Correct |
| Biological process | cell surface receptor signaling pathway · GO:0007166 | GO:0007166 cell surface receptor signaling pathway | Correct |
| Biological process | adrenergic receptor signaling pathway · GO:0071875 | GO:0071875 adrenergic receptor signaling pathway | Correct |
| Biological process | negative regulation of G protein-coupled receptor signaling pathway · GO:0045744 | GO:0045744 negative regulation of G protein-coupled receptor signaling pathway | Correct |
| Biological process | positive regulation of autophagosome maturation · GO:1901098 | GO:0010508 positive regulation of autophagy | Correct |
| Biological process | adenylate cyclase-modulating G protein-coupled receptor signaling pathway · GO:0007188 | GO:0007188 adenylate cyclase-modulating G protein-coupled receptor signaling pathway | Correct |
| Biological process | No annotation in UniProt | GO:2000273 positive regulation of signaling receptor activity | Speculative |
| Biological process | positive regulation of autophagosome maturation · GO:1901098 | GO:0043243 positive regulation of protein-containing complex disassembly | Correct |
| Biological process | No annotation in UniProt | GO:0065003 protein-containing complex assembly | Speculative |
| Biological process | No annotation in UniProt | GO:0010738 regulation of protein kinase A signaling | Speculative |
| Biological process | endosome to lysosome transport · GO:0008333 | GO:0008333 endosome to lysosome transport | Correct |
| Biological process | cell surface receptor signaling pathway · GO:0007166 | GO:0007169 transmembrane receptor protein tyrosine kinase signaling pathway | Correct |
| Biological process | positive regulation of MAPK cascade · GO:0043410 | GO:0043410 positive regulation of MAPK cascade | Correct |
| Biological process | No annotation in UniProt | GO:2000311 regulation of AMPA receptor activity | Speculative |
| Biological process | positive regulation of autophagosome maturation · GO:1901098 | GO:1901098 positive regulation of autophagosome maturation | Correct |
| Biological process | negative regulation of G protein-coupled receptor signaling pathway · GO:0045744 | GO:0002029 desensitization of G protein-coupled receptor signaling pathway | Correct |
| Biological process | No annotation in UniProt | GO:0032091 negative regulation of protein binding | Speculative |
| Biological process | cellular response to amyloid-beta · GO:1904646 | GO:1904646 cellular response to amyloid-beta | Correct |
| Biological process | receptor-mediated endocytosis · GO:0006898 | GO:0006898 receptor-mediated endocytosis | Correct |
| Biological process | No annotation in UniProt | GO:0007190 activation of adenylate cyclase activity | Speculative |
| Biological process | No annotation in UniProt | GO:1901653 cellular response to peptide | Speculative |
| Biological process | No annotation in UniProt | GO:2000479 regulation of cAMP-dependent protein kinase activity | Speculative |
| Cellular component | signaling receptor complex · GO:0043235 | GO:0043235 receptor complex | Correct |
| Cellular component | Golgi apparatus · GO:0005794 | GO:0005794 Golgi apparatus | Correct |
| Cellular component | plasma membrane · GO:0005886 | GO:0005886 plasma membrane | Correct |
| Cellular component | endosome membrane · GO:0010008 | GO:0010008 endosome membrane | Correct |
| Cellular component | lysosome · GO:0005764 | GO:0005764 lysosome | Correct |
| Cellular component | clathrin-coated endocytic vesicle membrane · GO:0030669 | GO:0030669 clathrin-coated endocytic vesicle membrane | Correct |
| Molecular function | norepinephrine binding · GO:0051380 | — | Missed |
| Biological process | positive regulation of glutamate receptor signaling pathway · GO:1900451 | — | Missed |
CA2 Carbonic anhydrase 2
P00918
8 correct · 2 missed · 2 speculativeProtein page →
67%correct8 correct · 2 missed · 2 speculative
CorrectMissedSpeculative
Known biology
- Carbonate dehydratase (CO2 hydration) · GO:0004089Correct
- Zinc ion binding (catalytic zinc) · GO:0008270Correct
- Esterase activity (secondary)Correct
- Bicarbonate transport coupling (transport metabolon)Correct
- Cytosol · GO:0005829Correct
- Cell membrane · GO:0005886Correct
- Apical part of cell · GO:0045177Correct
- Extracellular exosome · GO:0070062Correct
- Bone resorption / osteoclast differentiation (CA2 loss causes osteopetrosis)Missed
- pH and bicarbonate handling in kidney and eye (renal tubular acidosis, aqueous humour secretion)Missed
Source: UniProt P00918 (CAH2_HUMAN), curated GO annotation
AI prediction
- GO:0004089 carbonate dehydratase activityCorrect
- GO:0008270 zinc ion bindingCorrect
- GO:0052689 carboxylic ester hydrolase activityCorrect
- GO:0044070 regulation of monoatomic anion transportCorrect
- GO:0005829 cytosolCorrect
- GO:0005886 plasma membraneCorrect
- GO:0045177 apical part of cellCorrect
- GO:0070062 extracellular exosomeCorrect
- GO:0007186 G protein-coupled receptor signaling pathwaySpeculative
- GO:1904385 cellular response to angiotensinSpeculative
BioReason-Pro
Item by item
| Aspect | Known biology | AI prediction | Verdict |
|---|---|---|---|
| Molecular function | Carbonate dehydratase (CO2 hydration) · GO:0004089 | GO:0004089 carbonate dehydratase activity | Correct |
| Molecular function | Zinc ion binding (catalytic zinc) · GO:0008270 | GO:0008270 zinc ion binding | Correct |
| Molecular function | Esterase activity (secondary) | GO:0052689 carboxylic ester hydrolase activity | Correct |
| Biological process | Bicarbonate transport coupling (transport metabolon) | GO:0044070 regulation of monoatomic anion transport | Correct |
| Cellular component | Cytosol · GO:0005829 | GO:0005829 cytosol | Correct |
| Cellular component | Cell membrane · GO:0005886 | GO:0005886 plasma membrane | Correct |
| Cellular component | Apical part of cell · GO:0045177 | GO:0045177 apical part of cell | Correct |
| Cellular component | Extracellular exosome · GO:0070062 | GO:0070062 extracellular exosome | Correct |
| Biological process | Bone resorption / osteoclast differentiation (CA2 loss causes osteopetrosis) | — | Missed |
| Biological process | pH and bicarbonate handling in kidney and eye (renal tubular acidosis, aqueous humour secretion) | — | Missed |
| Biological process | No established role | GO:0007186 G protein-coupled receptor signaling pathway | Speculative |
| Biological process | No established role | GO:1904385 cellular response to angiotensin | Speculative |
LDHA L-lactate dehydrogenase A chain
P00338
11 correct · 0 missed · 0 speculativeProtein page →
100%correct11 correct · 0 missed · 0 speculative
CorrectMissedSpeculative
Known biology
- L-lactate dehydrogenase (NAD+) activity · GO:0004459Correct
- identical protein binding · GO:0042802Correct
- cadherin binding · GO:0045296Correct
- lactate metabolic process · GO:0006089Correct
- glycolytic process · GO:0006096Correct
- substantia nigra development · GO:0021762Correct
- cytosol · GO:0005829Correct
- membrane · GO:0016020Correct
- extracellular exosome · GO:0070062Correct
- oxidoreductase complex · GO:1990204Correct
- nucleus · GO:0005634Correct
Source: UniProt P00338, GO annotations (all evidence for "correct"; experimental evidence for "missed", max 2 per aspect shown)
AI prediction
- GO:0004457 lactate dehydrogenase activityCorrect
- GO:0042802 identical protein bindingCorrect
- GO:0045296 cadherin bindingCorrect
- GO:0006089 lactate metabolic processCorrect
- GO:0006090 pyruvate metabolic processCorrect
- GO:0021762 substantia nigra developmentCorrect
- GO:0005829 cytosolCorrect
- GO:0016020 membraneCorrect
- GO:0070062 extracellular exosomeCorrect
- GO:1990204 oxidoreductase complexCorrect
- GO:0005634 nucleusCorrect
BioReason-Pro
Item by item
| Aspect | Known biology | AI prediction | Verdict |
|---|---|---|---|
| Molecular function | L-lactate dehydrogenase (NAD+) activity · GO:0004459 | GO:0004457 lactate dehydrogenase activity | Correct |
| Molecular function | identical protein binding · GO:0042802 | GO:0042802 identical protein binding | Correct |
| Molecular function | cadherin binding · GO:0045296 | GO:0045296 cadherin binding | Correct |
| Biological process | lactate metabolic process · GO:0006089 | GO:0006089 lactate metabolic process | Correct |
| Biological process | glycolytic process · GO:0006096 | GO:0006090 pyruvate metabolic process | Correct |
| Biological process | substantia nigra development · GO:0021762 | GO:0021762 substantia nigra development | Correct |
| Cellular component | cytosol · GO:0005829 | GO:0005829 cytosol | Correct |
| Cellular component | membrane · GO:0016020 | GO:0016020 membrane | Correct |
| Cellular component | extracellular exosome · GO:0070062 | GO:0070062 extracellular exosome | Correct |
| Cellular component | oxidoreductase complex · GO:1990204 | GO:1990204 oxidoreductase complex | Correct |
| Cellular component | nucleus · GO:0005634 | GO:0005634 nucleus | Correct |
SLC2A1 Solute carrier family 2, facilitated glucose transporter member 1 (GLUT1)
P11166
22 correct · 4 missed · 2 speculativeProtein page →
79%correct22 correct · 4 missed · 2 speculative
CorrectMissedSpeculative
Known biology
- dehydroascorbic acid transmembrane transporter activity · GO:0033300Correct
- long-chain fatty acid transmembrane transporter activity · GO:0005324Correct
- identical protein binding · GO:0042802Correct
- D-glucose transmembrane transporter activity · GO:0055056Correct
- D-glucose transmembrane transporter activity · GO:0055056Correct
- L-ascorbic acid metabolic process · GO:0019852Correct
- L-ascorbic acid metabolic process · GO:0019852Correct
- D-glucose transmembrane transporter activity · GO:0055056Correct
- D-glucose import across plasma membrane · GO:0098708Correct
- central nervous system development · GO:0007417Correct
- L-ascorbic acid metabolic process · GO:0019852Correct
- transport across blood-brain barrier · GO:0150104Correct
- long-chain fatty acid import across plasma membrane · GO:0015911Correct
- D-glucose transmembrane transport · GO:1904659Correct
- blood microparticle · GO:0072562Correct
- midbody · GO:0030496Correct
- apical plasma membrane · GO:0016324Correct
- apical plasma membrane · GO:0016324Correct
- extracellular exosome · GO:0070062Correct
- basolateral plasma membrane · GO:0016323Correct
- Golgi membrane · GO:0000139Correct
- cortical actin cytoskeleton · GO:0030864Correct
- glucose transporter complex · GO:1990350Missed
- melanosome · GO:0042470Missed
- photoreceptor cell maintenance · GO:0045494Missed
- protein-containing complex assembly · GO:0065003Missed
Source: UniProt P11166, GO annotations (all evidence for "correct"; experimental evidence for "missed", max 2 per aspect shown)
AI prediction
- GO:0090482 vitamin transmembrane transporter activityCorrect
- GO:0005324 long-chain fatty acid transporter activityCorrect
- GO:0042802 identical protein bindingCorrect
- GO:0043621 protein self-associationSpeculative
- GO:0015149 hexose transmembrane transporter activityCorrect
- GO:0005355 glucose transmembrane transporter activitySpeculative
- GO:0055056 D-glucose transmembrane transporter activityCorrect
- GO:0005996 monosaccharide metabolic processCorrect
- GO:0005975 carbohydrate metabolic processCorrect
- GO:0034219 carbohydrate transmembrane transportCorrect
- GO:0098704 carbohydrate import across plasma membraneCorrect
- GO:0007417 central nervous system developmentCorrect
- GO:0019852 L-ascorbic acid metabolic processCorrect
- GO:0150104 transport across blood-brain barrierCorrect
- GO:0044539 long-chain fatty acid import into cellCorrect
- GO:1904659 glucose transmembrane transportCorrect
- GO:0072562 blood microparticleCorrect
- GO:0030496 midbodyCorrect
- GO:0045177 apical part of cellCorrect
- GO:0016324 apical plasma membraneCorrect
- GO:0070062 extracellular exosomeCorrect
- GO:0016323 basolateral plasma membraneCorrect
- GO:0000139 Golgi membraneCorrect
- GO:0030864 cortical actin cytoskeletonCorrect
BioReason-Pro
Item by item
| Aspect | Known biology | AI prediction | Verdict |
|---|---|---|---|
| Molecular function | dehydroascorbic acid transmembrane transporter activity · GO:0033300 | GO:0090482 vitamin transmembrane transporter activity | Correct |
| Molecular function | long-chain fatty acid transmembrane transporter activity · GO:0005324 | GO:0005324 long-chain fatty acid transporter activity | Correct |
| Molecular function | identical protein binding · GO:0042802 | GO:0042802 identical protein binding | Correct |
| Molecular function | No annotation in UniProt | GO:0043621 protein self-association | Speculative |
| Molecular function | D-glucose transmembrane transporter activity · GO:0055056 | GO:0015149 hexose transmembrane transporter activity | Correct |
| Molecular function | No annotation in UniProt | GO:0005355 glucose transmembrane transporter activity | Speculative |
| Molecular function | D-glucose transmembrane transporter activity · GO:0055056 | GO:0055056 D-glucose transmembrane transporter activity | Correct |
| Biological process | L-ascorbic acid metabolic process · GO:0019852 | GO:0005996 monosaccharide metabolic process | Correct |
| Biological process | L-ascorbic acid metabolic process · GO:0019852 | GO:0005975 carbohydrate metabolic process | Correct |
| Biological process | D-glucose transmembrane transporter activity · GO:0055056 | GO:0034219 carbohydrate transmembrane transport | Correct |
| Biological process | D-glucose import across plasma membrane · GO:0098708 | GO:0098704 carbohydrate import across plasma membrane | Correct |
| Biological process | central nervous system development · GO:0007417 | GO:0007417 central nervous system development | Correct |
| Biological process | L-ascorbic acid metabolic process · GO:0019852 | GO:0019852 L-ascorbic acid metabolic process | Correct |
| Biological process | transport across blood-brain barrier · GO:0150104 | GO:0150104 transport across blood-brain barrier | Correct |
| Biological process | long-chain fatty acid import across plasma membrane · GO:0015911 | GO:0044539 long-chain fatty acid import into cell | Correct |
| Biological process | D-glucose transmembrane transport · GO:1904659 | GO:1904659 glucose transmembrane transport | Correct |
| Cellular component | blood microparticle · GO:0072562 | GO:0072562 blood microparticle | Correct |
| Cellular component | midbody · GO:0030496 | GO:0030496 midbody | Correct |
| Cellular component | apical plasma membrane · GO:0016324 | GO:0045177 apical part of cell | Correct |
| Cellular component | apical plasma membrane · GO:0016324 | GO:0016324 apical plasma membrane | Correct |
| Cellular component | extracellular exosome · GO:0070062 | GO:0070062 extracellular exosome | Correct |
| Cellular component | basolateral plasma membrane · GO:0016323 | GO:0016323 basolateral plasma membrane | Correct |
| Cellular component | Golgi membrane · GO:0000139 | GO:0000139 Golgi membrane | Correct |
| Cellular component | cortical actin cytoskeleton · GO:0030864 | GO:0030864 cortical actin cytoskeleton | Correct |
| Cellular component | glucose transporter complex · GO:1990350 | — | Missed |
| Cellular component | melanosome · GO:0042470 | — | Missed |
| Biological process | photoreceptor cell maintenance · GO:0045494 | — | Missed |
| Biological process | protein-containing complex assembly · GO:0065003 | — | Missed |
VIM Vimentin
P08670
12 correct · 3 missed · 0 speculativeProtein page →
80%correct12 correct · 3 missed · 0 speculative
CorrectMissedSpeculative
Known biology
- molecular adaptor activity · GO:0060090Correct
- structural constituent of cytoskeleton · GO:0005200Correct
- identical protein binding · GO:0042802Correct
- scaffold protein binding · GO:0097110Correct
- protein domain specific binding · GO:0019904Correct
- double-stranded RNA binding · GO:0003725Correct
- positive regulation of collagen biosynthetic process · GO:0032967Correct
- regulation of mRNA stability · GO:0043488Correct
- cellular response to lipopolysaccharide · GO:0071222Correct
- positive regulation of gene expression · GO:0010628Correct
- cellular response to muramyl dipeptide · GO:0071225Correct
- intermediate filament cytoskeleton · GO:0045111Correct
- cytosol · GO:0005829Missed
- extracellular exosome · GO:0070062Missed
- keratin filament binding · GO:1990254Missed
Source: UniProt P08670, GO annotations (all evidence for "correct"; experimental evidence for "missed", max 2 per aspect shown)
AI prediction
- GO:0060090 molecular adaptor activityCorrect
- GO:0005200 structural constituent of cytoskeletonCorrect
- GO:0042802 identical protein bindingCorrect
- GO:0097110 scaffold protein bindingCorrect
- GO:0019904 protein domain specific bindingCorrect
- GO:0003725 double-stranded RNA bindingCorrect
- GO:0032967 positive regulation of collagen biosynthetic processCorrect
- GO:0043488 regulation of mRNA stabilityCorrect
- GO:0071222 cellular response to lipopolysaccharideCorrect
- GO:0045727 positive regulation of translationCorrect
- GO:0032495 response to muramyl dipeptideCorrect
- GO:0045111 intermediate filament cytoskeletonCorrect
BioReason-Pro
Item by item
| Aspect | Known biology | AI prediction | Verdict |
|---|---|---|---|
| Molecular function | molecular adaptor activity · GO:0060090 | GO:0060090 molecular adaptor activity | Correct |
| Molecular function | structural constituent of cytoskeleton · GO:0005200 | GO:0005200 structural constituent of cytoskeleton | Correct |
| Molecular function | identical protein binding · GO:0042802 | GO:0042802 identical protein binding | Correct |
| Molecular function | scaffold protein binding · GO:0097110 | GO:0097110 scaffold protein binding | Correct |
| Molecular function | protein domain specific binding · GO:0019904 | GO:0019904 protein domain specific binding | Correct |
| Molecular function | double-stranded RNA binding · GO:0003725 | GO:0003725 double-stranded RNA binding | Correct |
| Biological process | positive regulation of collagen biosynthetic process · GO:0032967 | GO:0032967 positive regulation of collagen biosynthetic process | Correct |
| Biological process | regulation of mRNA stability · GO:0043488 | GO:0043488 regulation of mRNA stability | Correct |
| Biological process | cellular response to lipopolysaccharide · GO:0071222 | GO:0071222 cellular response to lipopolysaccharide | Correct |
| Biological process | positive regulation of gene expression · GO:0010628 | GO:0045727 positive regulation of translation | Correct |
| Biological process | cellular response to muramyl dipeptide · GO:0071225 | GO:0032495 response to muramyl dipeptide | Correct |
| Cellular component | intermediate filament cytoskeleton · GO:0045111 | GO:0045111 intermediate filament cytoskeleton | Correct |
| Cellular component | cytosol · GO:0005829 | — | Missed |
| Cellular component | extracellular exosome · GO:0070062 | — | Missed |
| Molecular function | keratin filament binding · GO:1990254 | — | Missed |