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New PDB Depositions vs. Their Blind AlphaFold Predictions — A Running Test of “Is Folding Solved?”

Release week 2023-12-20

125
structures analysed (11 full · 8.8%)
32.4%
confidently wrong
10.8%
novel sequences
00.0%
novel & wrong
0.964
median TM-score

Zoomed into the red "confidently wrong" box above (pLDDT ≥ 70, TM < 0.5) — the structures AlphaFold got confidently wrong.

The worst offenders ranked, one row per protein (AlphaFold has one model per sequence, so repeat depositions are collapsed — “×N” marks how many structures of that protein exist; the worst is shown). Each row joins what AlphaFold claimed (blue, pLDDT/100) to what the experiment showed (red, TM-score) — the longer the bar, the bigger the miss. Hover a dot to preview its Cα-deviation ribbon; click to open the full entry.

How to read this

Every point is one experimental protein structure. The horizontal axis is AlphaFold's own confidence in its prediction (mean pLDDT, 0–100). The vertical axis is how well that blind prediction actually matches the experiment (TM-score, 0–1; above 0.5 means the same fold, above 0.9 near-identical). Marker size grows with the FRAUD score (confidence-weighted error).

Cutoff: the shaded red box is the "confidently wrong" zone — AlphaFold was confident (mean pLDDT above 70) yet the fold is wrong (TM-score below 0.5). A predictor that had truly solved folding would leave that box empty.

Take-home: 3 of 125 structures (2.4%) are confidently wrong; median TM-score is 0.964.

Read moreShow less — how each metric is calculated

TM-score: how similar the two 3D shapes are overall, 0–1 (a random pair scores ~0.17, an identical fold ~1). Length-normalised so large and small proteins compare fairly. TM = (1/L) Σᵢ 1/(1 + (dᵢ/d₀)²) — dᵢ is the gap between the i-th aligned Cα atoms after best-fit superposition, and d₀ = 1.24(L−15)^⅓ − 1.8 sets the distance scale for length L. Ref: Zhang & Skolnick, Proteins 2004 doi:10.1002/prot.20264; computed with TM-align, doi:10.1093/nar/gki524.

pLDDT: AlphaFold's own confidence in each residue, 0–100 (higher = surer). It is the model predicting its own accuracy before ever seeing the experiment. We plot the per-structure mean. pLDDT = (1/N) Σᵢ pLDDTᵢ, where pLDDTᵢ is the network's confidence output for residue i.

FRAUD score: the headline number — how wrong the prediction was, weighted by how confident AlphaFold was, so a big error it was sure about counts most. FRAUD = (1/N) Σᵢ (pLDDTᵢ/100) · min(Δᵢ,15)/15, where Δᵢ is residue i's Cα distance from the experiment (Å) after superposition, capped at 15 Å. Runs 0 (perfect) to 1.

Novelty: how little AlphaFold had to go on — 100 minus the highest sequence identity between this protein and any structure released before the 2018-04-30 training cutoff. High = genuinely unseen (100% = nothing similar was ever in the training set). novelty = 100 − maxₚ identity(s, p) over pre-cutoff PDB chains p, with identity = 100 × (matching aligned residues)/(alignment length), from an MMseqs2 search.

Homology: the point colour. High novelty (above 70%) flags the sequence as novel (amber) — AlphaFold had no close template; otherwise a pre-cutoff homolog existed (blue) it could have learned the fold from. novel ⇔ novelty > 70%.

What the metrics mean

TM-score (0–1): overall fold match — above 0.5 is the same fold, above 0.9 near-identical. Cα-RMSD (Å): average backbone distance after best-fit superposition — lower is better (under 2 Å is excellent). lDDT (0–1): local accuracy measured without superposition — above 0.8 is good. Each bar counts how many structures fall in that range.

Take-home: median TM-score 0.964 — most predictions match the experimental fold well, with a long tail that do not.

Read moreShow less — how each metric is calculated

TM-score: overall shape match, 0–1 (above 0.5 = same fold, above 0.9 near-identical), length-normalised. TM = (1/L) Σᵢ 1/(1 + (dᵢ/d₀)²) with dᵢ the aligned-Cα gap after superposition and d₀ = 1.24(L−15)^⅓ − 1.8. Ref: Zhang & Skolnick, Proteins 2004 doi:10.1002/prot.20264.

Cα-RMSD: the average straight-line distance between matching backbone Cα atoms once the two structures are best-fit superposed (Å; lower is better, under ~2 Å excellent). RMSD = √( (1/N) Σᵢ |Pᵢ − (R·Qᵢ + t)|² ), with Pᵢ/Qᵢ the experimental/model Cα coordinates and R,t the rotation and translation from Kabsch superposition.

lDDT: local accuracy with no superposition — the fraction of short-range inter-residue distances the model reproduces, so it is not fooled by a single wrongly-placed domain. lDDT = (1/N) Σᵢ ¼ Σ_t 1[ |d_exp − d_model| < t ] over thresholds t ∈ {0.5, 1, 2, 4} Å and all residue pairs within 15 Å.

Trend over time

The blue line is the mean TM-score of the structures by their deposit month; the red bars count how many were confidently wrong. Binning by deposit date (rather than by when we processed them) gives an even timeline, tracking whether AlphaFold's accuracy on newly-deposited structures is holding steady, improving, or slipping as the PDB keeps growing. Months with fewer than 5 structures are omitted so each point is a meaningful average. A dashed trend line is drawn only if the change over time is statistically significant.

Read moreShow less — how each metric is calculated

Mean TM-score: the month's average shape-match score. TM̄ = (1/M) Σ TM over the M structures deposited that month.

Trend line: a monotonic-trend test over the monthly means — Mann-Kendall (Kendall's τ) for significance, with a robust Theil-Sen slope for the line. Rank-based, so it tolerates the skewed TM distribution and noisy low-count months. Shown only when p < 0.05; otherwise a note reports that no significant trend was found.

Confidently wrong: the count that were both confident and wrong. count( mean pLDDT > 70 AND TM < 0.5 ).

Matched structures

PDBUniProtProteinMethodÅDeposited Novelty %pLDDTTMlDDTGDT_TSRMSDFRAUDFlag
8W77_A P0ABE7 Human Consensus Olfactory Receptor OR52c i EM 3.61 2023-08-30 90.56 0.28 0.65 wrong
8IB8_Q Q9H2J4 Phosducin-like protein 3 EM 4.42 2023-02-09 39.40 83.78 0.67 0.77 6.19 13.88 0.61 ok
8HN0_A Q14162 Scavenger receptor class F member 1 X-ray 2.20 2022-12-06 73.60 novel 88.78 0.55 0.88 18.64 8.18 0.44 ok
8TER_A Q92734 TRK-fused gene protein Low Complexity Doma EM 2.59 2023-07-06 4.00 42.45 0.32 0.55 5.00 17.22 0.34 ok
8TEQ_0 Q92734 TRK-fused gene protein Low Complexity Doma EM 2.84 2023-07-06 4.00 42.50 0.22 0.46 10.34 13.01 0.29 ok
8HNA_B Q14162 Scavenger receptor class F member 1 X-ray 2.60 2022-12-07 68.00 91.10 0.65 0.84 39.54 5.94 0.28 ok
8I9Q_Q Q9H2J4 Phosducin-like protein 3 EM 4.22 2023-02-07 79.69 0.70 0.24 ok
8FJA_C P43358 Melanoma-associated antigen 4 peptide EM 3.00 2022-12-19 90.90 0.29 0.69 40.00 4.25 0.23 wrong
8J46_A P0ABE7 Olfactory receptor OR52c,Soluble cytochrom EM 3.66 2023-04-19 53.90 90.38 0.27 0.73 47.27 5.71 0.21 wrong
8IB8_S P60709 ACTB protein (Fragment) EM 4.42 2023-02-09 95.19 0.78 0.21 ok
8HSF_B P01308 Insulin B chain X-ray 2.90 2022-12-19 10.00 49.07 0.52 0.45 30.56 6.84 0.18 ok
8HSK_B P01308 Insulin B chain X-ray 1.64 2022-12-19 3.50 48.30 0.39 0.44 32.50 6.45 0.18 ok
8HOC_A P63096 Guanine nucleotide-binding protein G(i) su EM 3.00 2022-12-09 93.75 0.81 0.18 ok
8UQR_A P04637 Cellular tumor antigen p53 X-ray 1.22 2023-10-24 75.06 0.76 0.18 ok
8HN8_A P63096 Guanine nucleotide-binding protein G(i) su EM 3.00 2022-12-07 93.75 0.81 0.18 ok
8HQ5_A P62826 GTP-binding nuclear protein Ran X-ray 2.25 2022-12-13 88.62 0.81 0.17 ok
8U1U_B P63096 Guanine nucleotide-binding protein G(i) su EM 3.10 2023-09-02 93.75 0.82 0.17 ok
8HQ4_A P62826 GTP-binding nuclear protein Ran X-ray 2.12 2022-12-13 88.62 0.81 0.17 ok
8HTI_A P63092 Guanine nucleotide-binding protein G(s) su EM 2.97 2022-12-21 91.31 0.82 0.17 ok
8I9Q_D P50991 T-complex protein 1 subunit delta EM 4.22 2023-02-07 89.69 0.82 0.16 ok
8IEO_P Q9NQ11 Polyamine-transporting ATPase 13A2 EM 3.78 2023-02-15 79.62 0.80 0.16 ok
8IEM_P Q9NQ11 Polyamine-transporting ATPase 13A2 EM 3.35 2023-02-15 79.62 0.82 0.15 ok
8HSK_A P01308 Insulin A chain X-ray 1.64 2022-12-19 0.00 51.25 0.31 0.46 42.86 4.89 0.14 ok
8WQR_A Q16531 DNA damage-binding protein 1 EM 3.08 2023-10-12 92.00 0.85 0.14 ok
8IEN_P Q9NQ11 Polyamine-transporting ATPase 13A2 EM 3.25 2023-02-15 79.62 0.83 0.14 ok
8HSF_A P01308 Insulin A chain X-ray 2.90 2022-12-19 0.00 51.41 0.31 0.53 47.50 4.46 0.13 ok
8HTI_G P59768 Guanine nucleotide-binding protein G(I)/G( EM 2.97 2022-12-21 89.56 0.87 0.12 ok
8IER_P Q9NQ11 Polyamine-transporting ATPase 13A2 EM 4.87 2023-02-15 79.62 0.85 0.12 ok
8HOC_G P59768 Guanine nucleotide-binding protein G(I)/G( EM 3.00 2022-12-09 89.56 0.89 0.10 ok
8HN8_G P59768 Guanine nucleotide-binding protein G(I)/G( EM 3.00 2022-12-07 89.56 0.90 0.09 ok
8IB8_D P50991 T-complex protein 1 subunit delta EM 4.42 2023-02-09 89.69 0.90 0.09 ok
8U1U_D P59768 Guanine nucleotide-binding protein G(I)/G( EM 3.10 2023-09-02 89.56 0.92 0.07 ok
8IEL_P Q9NQ11 Polyamine-transporting ATPase 13A2 EM 5.65 2023-02-15 79.62 0.92 0.07 ok
8IES_P Q9NQ11 Polyamine-transporting ATPase 13A2 EM 3.73 2023-02-15 79.62 0.92 0.06 ok
8G4Y_A Q9ULT6 E3 ubiquitin-protein ligase ZNRF3 X-ray 1.41 2023-02-10 50.72 0.89 0.06 ok
8IB8_C P49368 T-complex protein 1 subunit gamma EM 4.42 2023-02-09 89.06 0.94 0.05 ok
8UN5_A P01116 GTPase KRas X-ray 1.31 2023-10-18 91.50 0.94 0.05 ok
8UN4_A P01116 GTPase KRas X-ray 1.57 2023-10-18 91.50 0.94 0.05 ok
8IB8_H P50990 T-complex protein 1 subunit theta EM 4.42 2023-02-09 87.69 0.94 0.05 ok
8IB8_E P48643 T-complex protein 1 subunit epsilon EM 4.42 2023-02-09 89.38 0.94 0.05 ok
8TDV_A Q9Y3Z3 Deoxynucleoside triphosphate triphosphohyd EM 3.44 2023-07-05 88.19 0.94 0.05 ok
8UN3_A P01116 GTPase KRas X-ray 2.07 2023-10-18 91.50 0.95 0.05 ok
8HRL_A Q9BYF1 Processed angiotensin-converting enzyme 2 EM 2.80 2022-12-15 90.69 0.95 0.05 ok
8IB8_G Q99832 T-complex protein 1 subunit eta EM 4.42 2023-02-09 88.88 0.95 0.04 ok
8BX6_A O60674 Tyrosine-protein kinase JAK2 X-ray 1.50 2022-12-08 86.88 0.95 0.04 ok
8BX9_A O60674 Tyrosine-protein kinase JAK2 X-ray 1.40 2022-12-08 86.88 0.95 0.04 ok
8OOJ_A P27707 Deoxycytidine kinase X-ray 2.10 2023-04-05 88.44 0.95 0.04 ok
8P45_A Q86WV6 Stimulator of interferon genes protein X-ray 3.23 2023-05-19 83.75 0.95 0.04 ok
8ORW_A Q86WV6 Stimulator of interferon protein X-ray 2.95 2023-04-17 83.75 0.95 0.04 ok
8HRZ_M Q9UNZ2 NSFL1 cofactor p47 X-ray 2.70 2022-12-16 74.06 0.95 0.04 ok
8UD9_D O14818 Proteasome subunit alpha type-7 EM 2.04 2023-09-28 94.38 0.96 0.04 ok
8BXH_A O60674 Tyrosine-protein kinase JAK2 X-ray 1.30 2022-12-08 86.88 0.96 0.04 ok
8OMR_B Q9H974 Queuine tRNA-ribosyltransferase accessory EM 3.30 2023-03-31 89.75 0.96 0.04 ok
8UD9_B P25787 Proteasome subunit alpha type-2 EM 2.04 2023-09-28 94.75 0.96 0.04 ok
8IB8_B P78371 T-complex protein 1 subunit beta EM 4.42 2023-02-09 89.81 0.96 0.04 ok
8WD4_A P00533 Epidermal growth factor receptor X-ray 2.55 2023-09-14 75.94 0.95 0.04 ok
8JWJ_B P62837 Ubiquitin-conjugating enzyme E2 D2 X-ray 2.96 2023-06-29 96.50 0.96 0.03 ok
8OMR_A Q9BXR0 Queuine tRNA-ribosyltransferase catalytic EM 3.30 2023-03-31 93.69 0.96 0.03 ok
8HRK_A Q9BYF1 Processed angiotensin-converting enzyme 2 EM 3.30 2022-12-15 90.69 0.96 0.03 ok
8HN1_A P35348 Alpha-1A adrenergic receptor EM 2.90 2022-12-06 70.31 0.95 0.03 ok
8UD9_E P28066 Proteasome subunit alpha type-5 EM 2.04 2023-09-28 94.12 0.96 0.03 ok
8IB8_A P17987 T-complex protein 1 subunit alpha EM 4.42 2023-02-09 89.00 0.96 0.03 ok
8IB8_F P40227 T-complex protein 1 subunit zeta EM 4.42 2023-02-09 89.88 0.96 0.03 ok
8A2X_A Q86WV6 Stimulator of interferon protein X-ray 3.00 2022-06-06 83.75 0.96 0.03 ok
8C8J_A O00370 RNA-directed DNA polymerase X-ray 2.10 2023-01-20 86.56 0.97 0.03 ok
8UD9_C P25789 Proteasome subunit alpha type-4 EM 2.04 2023-09-28 93.50 0.97 0.03 ok
8HR0_C O75396 Vesicle-trafficking protein SEC22b X-ray 3.34 2022-12-14 83.50 0.97 0.02 ok
8HPP_C Q9NXZ1 Sarcoma antigen 1 X-ray 3.00 2022-12-12 50.19 0.95 0.02 ok
8K9R_B P08174 Green fluorescent protein,Complement decay EM 2.68 2023-08-01 78.25 0.97 0.02 ok
8HPP_A Q68E01 Integrator complex subunit 3 X-ray 3.00 2022-12-12 83.06 0.97 0.02 ok
8HRZ_A P55072 Transitional endoplasmic reticulum ATPase X-ray 2.70 2022-12-16 82.56 0.97 0.02 ok
8UW3_A O00370 LINE-1 retrotransposable element ORF2 prot EM 3.20 2023-11-06 86.56 0.97 0.02 ok
8BXC_A O60674 Tyrosine-protein kinase JAK2 X-ray 1.90 2022-12-08 86.88 0.98 0.02 ok
8HRN_A Q9BYF1 Angiotensin-converting enzyme 2 EM 3.90 2022-12-15 90.69 0.98 0.02 ok
8HRU_A Q9BYF1 Angiotensin-converting enzyme 2 EM 3.90 2022-12-16 90.69 0.98 0.02 ok
8WQR_B Q9C0C7 Activating molecule in BECN1-regulated aut EM 3.08 2023-10-12 48.75 0.96 0.02 ok
8FJA_A Q861F7 MHC class I antigen EM 3.00 2022-12-19 88.19 0.98 0.02 ok
8FJA_B P61769 Beta-2-microglobulin EM 3.00 2022-12-19 94.06 0.98 0.02 ok
8FJB_B P61769 Beta-2-microglobulin EM 3.06 2022-12-19 94.06 0.98 0.01 ok
8FJB_A Q861F7 MHC class I antigen EM 3.06 2022-12-19 88.19 0.98 0.01 ok
8UD9_L P28074 Proteasome subunit beta type-5 EM 2.04 2023-09-28 82.38 0.98 0.01 ok
8HR0_B O95486 Protein transport protein Sec24A X-ray 3.34 2022-12-14 75.50 0.98 0.01 ok
8X6P_A P62942 Peptidyl-prolyl cis-trans isomerase FKBP1A X-ray 1.05 2023-11-21 96.25 0.99 0.01 ok
8UD9_I Q99436 Proteasome subunit beta type-7 EM 2.04 2023-09-28 90.38 0.99 0.01 ok
8K9T_B P08174 Green fluorescent protein,Complement decay EM 2.66 2023-08-01 78.25 0.99 0.01 ok
8UD9_G P25788 Proteasome subunit alpha type-3 EM 2.04 2023-09-28 94.50 0.99 0.01 ok
8HTI_B P62873 Guanine nucleotide-binding protein G(I)/G( EM 2.97 2022-12-21 97.06 0.99 0.01 ok
8UJY_A P61964 WD repeat-containing protein 5 X-ray 2.01 2023-10-11 93.31 0.99 0.01 ok
8HOC_B P62873 Guanine nucleotide-binding protein G(I)/G( EM 3.00 2022-12-09 97.06 0.99 0.01 ok
8FH8_A P15121 Aldo-keto reductase family 1 member B1 X-ray 1.60 2022-12-13 98.31 0.99 0.01 ok
7Y2R_A P00918 Carbonic anhydrase 2 X-ray 1.20 2022-06-09 97.38 0.99 0.01 ok
7Y2W_A P00918 Carbonic anhydrase 2 X-ray 1.20 2022-06-09 97.38 0.99 0.01 ok
7Y2U_A P00918 Carbonic anhydrase 2 X-ray 1.20 2022-06-09 97.38 0.99 0.01 ok
7Y2S_A P00918 Carbonic anhydrase 2 X-ray 1.20 2022-06-09 97.38 0.99 0.01 ok
8UD9_H P28072 Proteasome subunit beta type-6 EM 2.04 2023-09-28 88.69 0.99 0.01 ok
8HN8_B P62873 Guanine nucleotide-binding protein G(I)/G( EM 3.00 2022-12-07 97.06 0.99 0.01 ok
8FH6_A P15121 Aldo-keto reductase family 1 member B1 X-ray 1.95 2022-12-13 98.31 0.99 0.01 ok
7Y2V_A P00918 Carbonic anhydrase 2 X-ray 1.20 2022-06-09 97.38 0.99 0.01 ok
7Y2T_A P00918 Carbonic anhydrase 2 X-ray 1.20 2022-06-09 97.38 0.99 0.01 ok
8U1U_C P62873 Guanine nucleotide-binding protein G(I)/G( EM 3.10 2023-09-02 97.06 0.99 0.01 ok
8HR0_A Q15436 Protein transport protein Sec23A X-ray 3.34 2022-12-14 92.69 0.99 0.01 ok
8FH9_A P15121 Aldo-keto reductase family 1 member B1 X-ray 1.70 2022-12-13 98.31 0.99 0.00 ok
8UD9_J P49720 Proteasome subunit beta type-3 EM 2.04 2023-09-28 97.31 1.00 0.00 ok
8FH5_A P15121 Aldo-keto reductase family 1 member B1 X-ray 1.62 2022-12-13 98.31 1.00 0.00 ok
7Y2X_A P00918 Carbonic anhydrase 2 X-ray 1.50 2022-06-09 97.38 1.00 0.00 ok
8UD9_A P60900 Proteasome subunit alpha type-6 EM 2.04 2023-09-28 96.06 1.00 0.00 ok
8FH7_A P15121 Aldo-keto reductase family 1 member B1 X-ray 1.45 2022-12-13 98.31 1.00 0.00 ok
8UD9_F P25786 Proteasome subunit alpha type-1 EM 2.04 2023-09-28 91.88 1.00 0.00 ok
8UD9_N P28070 Proteasome subunit beta type-4 EM 2.04 2023-09-28 87.44 1.00 0.00 ok
7Y2A_A P00918 Carbonic anhydrase 2 X-ray 1.20 2022-06-09 97.38 1.00 0.00 ok
7Y2C_A P00918 Carbonic anhydrase 2 X-ray 1.20 2022-06-09 97.38 1.00 0.00 ok
7Y2J_A P00918 Carbonic anhydrase 2 X-ray 1.25 2022-06-09 97.38 1.00 0.00 ok
7Y2F_A P00918 Carbonic anhydrase 2 X-ray 1.20 2022-06-09 97.38 1.00 0.00 ok
7Y2E_A P00918 Carbonic anhydrase 2 X-ray 1.20 2022-06-09 97.38 1.00 0.00 ok
7Y2Q_A P00918 Carbonic anhydrase 2 X-ray 1.35 2022-06-09 97.38 1.00 0.00 ok
7Y2O_A P00918 Carbonic anhydrase 2 X-ray 1.25 2022-06-09 97.38 1.00 0.00 ok
7Y2N_A P00918 Carbonic anhydrase 2 X-ray 1.25 2022-06-09 97.38 1.00 0.00 ok
7Y2M_A P00918 Carbonic anhydrase 2 X-ray 1.25 2022-06-09 97.38 1.00 0.00 ok
7Y2L_A P00918 Carbonic anhydrase 2 X-ray 1.25 2022-06-09 97.38 1.00 0.00 ok
7Y2K_A P00918 Carbonic anhydrase 2 X-ray 1.25 2022-06-09 97.38 1.00 0.00 ok
7Y2I_A P00918 Carbonic anhydrase 2 X-ray 1.40 2022-06-09 97.38 1.00 0.00 ok
7Y2H_A P00918 Carbonic anhydrase 2 X-ray 1.20 2022-06-09 97.38 1.00 0.00 ok
7Y2G_A P00918 Carbonic anhydrase 2 X-ray 1.20 2022-06-09 97.38 1.00 0.00 ok
8UD9_M P20618 Proteasome subunit beta type-1 EM 2.04 2023-09-28 91.38 1.00 0.00 ok
8UD9_K P49721 Proteasome subunit beta type-2 EM 2.04 2023-09-28 96.69 1.00 0.00 ok

Click a column header to sort. FRAUD = confidence-weighted error; a structure is flagged confidently wrong when mean pLDDT > 70 yet TM-score < 0.5.