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

Release week 2023-11-29

125
structures analysed (11 full · 8.8%)
00.0%
confidently wrong
00.0%
novel sequences
00.0%
novel & wrong
0.944
median TM-score

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

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: 0 of 125 structures (0.0%) are confidently wrong; median TM-score is 0.944.

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 0.944 — 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
8J6K_B Q14116 Interleukin-18 X-ray 3.12 2023-04-26 0.00 90.05 0.68 0.52 1.64 22.27 0.83 ok
8PMJ_A O95342 Bile salt export pump EM 2.81 2023-06-28 49.00 88.84 0.69 0.78 14.10 8.64 0.48 ok
8OLG_A P05067 Amyloid-beta protein 42 EM 4.20 2023-03-30 4.80 45.82 0.31 0.47 0.00 17.84 0.41 ok
8J00_E P0DP23 Calmodulin-1 EM 3.00 2023-04-09 85.25 0.52 0.41 ok
8OLN_A P05067 Amyloid-beta protein 42 EM 3.30 2023-03-30 4.80 42.72 0.33 0.54 0.00 17.60 0.40 ok
8OLQ_A P05067 Amyloid-beta protein 42 EM 4.00 2023-03-30 4.80 40.15 0.29 0.45 1.56 19.45 0.37 ok
8OLO_A P05067 Amyloid-beta protein 42 EM 3.50 2023-03-30 0.00 51.04 0.28 0.44 15.32 12.62 0.34 ok
8OL5_A P05067 Amyloid-beta protein 42 EM 3.40 2023-03-30 0.00 54.66 0.23 0.44 17.74 10.34 0.33 ok
8OL2_A P05067 Amyloid-beta protein 42 EM 3.00 2023-03-30 0.00 54.66 0.24 0.43 17.74 10.33 0.33 ok
8OL6_A P05067 Amyloid-beta protein 42 EM 3.80 2023-03-30 0.00 54.66 0.25 0.43 17.74 10.21 0.33 ok
7XUZ_A P56524 Histone deacetylase 4 X-ray 3.59 2022-05-20 0.00 81.97 0.68 0.84 30.63 6.28 0.30 ok
8ASE_A P00734 Thrombin light chain X-ray 2.55 2022-08-19 83.94 0.74 0.22 ok
8OL7_A P05067 Amyloid-beta protein 42 EM 3.00 2023-03-30 2.40 50.41 0.28 0.57 25.00 6.89 0.22 ok
8HNK_L O14625 C-X-C motif chemokine 11 EM 3.01 2022-12-08 79.94 0.73 0.21 ok
8HNM_A P63096 Guanine nucleotide-binding protein G(i) su EM 2.94 2022-12-08 93.75 0.81 0.18 ok
8HNK_A P63096 Guanine nucleotide-binding protein G(i) su EM 3.01 2022-12-08 93.75 0.81 0.18 ok
8HNL_A P63096 Guanine nucleotide-binding protein G(i) su EM 2.98 2022-12-08 93.75 0.81 0.18 ok
8K2X_A P63096 Guanine nucleotide-binding protein G(i) su EM 3.20 2023-07-14 93.75 0.81 0.18 ok
8CR1_A O43681 ATPase ASNA1 EM 3.20 2023-03-07 79.19 0.82 0.15 ok
8CQZ_B O00258 Guided entry of tail-anchored proteins fac X-ray 2.80 2023-03-07 77.69 0.82 0.14 ok
8CQZ_A O43681 ATPase ASNA1 X-ray 2.80 2023-03-07 79.19 0.83 0.14 ok
8OX5_A O43520 Phospholipid-transporting ATPase IC EM 2.90 2023-05-01 80.38 0.83 0.13 ok
8OX4_A O43520 Phospholipid-transporting ATPase IC EM 3.40 2023-05-01 80.38 0.84 0.13 ok
8F8M_B Q15596 Nuclear receptor coactivator 2 X-ray 2.60 2022-11-22 47.59 0.79 0.10 ok
8DPT_C Q14626 Interleukin-11 receptor subunit alpha EM 4.00 2022-07-17 81.56 0.89 0.09 ok
8OQH_A Q86T03 Type 1 phosphatidylinositol 4,5-bisphospha X-ray 1.76 2023-04-12 69.38 0.87 0.09 ok
8OXB_A O43520 Phospholipid-transporting ATPase IC EM 2.99 2023-05-01 80.38 0.89 0.09 ok
8OXC_A O43520 Phospholipid-transporting ATPase IC EM 2.58 2023-05-01 80.38 0.89 0.09 ok
8OXA_A O43520 Phospholipid-transporting ATPase IC EM 2.76 2023-05-01 80.38 0.89 0.09 ok
8J00_A O43526 Potassium voltage-gated channel subfamily EM 3.00 2023-04-09 58.19 0.85 0.09 ok
8JTC_A Q05940 Synaptic vesicular amine transporter EM 3.52 2023-06-21 77.69 0.90 0.08 ok
8HKE_A Q9GZC8 Systemic RNA interference defective protei EM 3.71 2022-11-25 76.31 0.90 0.08 ok
8ASE_B P00734 Thrombin heavy chain X-ray 2.55 2022-08-19 83.94 0.91 0.08 ok
8JSW_A Q05940 Synaptic vesicular amine transporter EM 2.84 2023-06-20 77.69 0.90 0.07 ok
8HIP_A Q9GZC8 Systemic RNA interference defective protei EM 2.77 2022-11-21 76.31 0.91 0.07 ok
8DPS_A P40189 Interleukin-6 receptor subunit beta EM 3.47 2022-07-17 74.62 0.91 0.07 ok
8K2X_G P59768 Guanine nucleotide-binding protein G(I)/G( EM 3.20 2023-07-14 89.56 0.92 0.07 ok
8CR2_A O43681 ATPase ASNA1 EM 4.20 2023-03-07 79.19 0.91 0.07 ok
8HNK_G P59768 Guanine nucleotide-binding protein G(I)/G( EM 3.01 2022-12-08 89.56 0.93 0.06 ok
8JTA_A Q05940 Synaptic vesicular amine transporter EM 3.36 2023-06-21 77.69 0.92 0.06 ok
8OX6_B Q9NV96 Cell cycle control protein 50A EM 2.39 2023-05-01 89.50 0.93 0.06 ok
8DPT_A P40189 Interleukin-6 receptor subunit beta EM 4.00 2022-07-17 74.62 0.91 0.06 ok
8OX5_B Q9NV96 Cell cycle control protein 50A EM 2.90 2023-05-01 89.50 0.93 0.06 ok
8IZY_A O43526 Potassium voltage-gated channel subfamily EM 2.50 2023-04-09 58.19 0.89 0.06 ok
8JT9_A Q05940 Synaptic vesicular amine transporter EM 2.97 2023-06-21 77.69 0.92 0.06 ok
8BOC_A P29317 Ephrin type-A receptor 2 X-ray 1.90 2022-11-15 82.25 0.93 0.06 ok
8DPS_C Q14626 Interleukin-11 receptor subunit alpha EM 3.47 2022-07-17 81.56 0.93 0.06 ok
8DPU_C Q14626 Interleukin-11 receptor subunit alpha X-ray 3.78 2022-07-17 81.56 0.93 0.06 ok
8OXB_B Q9NV96 Cell cycle control protein 50A EM 2.99 2023-05-01 89.50 0.94 0.06 ok
8OX4_B Q9NV96 Cell cycle control protein 50A EM 3.40 2023-05-01 89.50 0.94 0.06 ok
8OX7_B Q9NV96 Cell cycle control protein 50A EM 2.56 2023-05-01 89.50 0.94 0.06 ok
8HNL_G P59768 Guanine nucleotide-binding protein G(I)/G( EM 2.98 2022-12-08 89.56 0.94 0.06 ok
8OXC_B Q9NV96 Cell cycle control protein 50A EM 2.58 2023-05-01 89.50 0.94 0.06 ok
8DPW_A P20809 Interleukin-11 X-ray 1.80 2022-07-17 82.62 0.93 0.06 ok
8OXA_B Q9NV96 Cell cycle control protein 50A EM 2.76 2023-05-01 89.50 0.94 0.06 ok
8OX9_B Q9NV96 Cell cycle control protein 50A EM 2.72 2023-05-01 89.50 0.94 0.06 ok
8OX8_B Q9NV96 Cell cycle control protein 50A EM 2.98 2023-05-01 89.50 0.94 0.05 ok
8HNM_G P59768 Guanine nucleotide-binding protein G(I)/G( EM 2.94 2022-12-08 89.56 0.95 0.05 ok
8DPT_B P20809 Interleukin-11 EM 4.00 2022-07-17 82.62 0.94 0.05 ok
8DPU_B P20809 Interleukin-11 X-ray 3.78 2022-07-17 82.62 0.94 0.05 ok
8OX8_A O43520 Phospholipid-transporting ATPase IC EM 2.98 2023-05-01 80.38 0.94 0.05 ok
8FMI_A P01116 Isoform 2B of GTPase KRas X-ray 1.12 2022-12-23 91.50 0.95 0.05 ok
8P0L_A O60502 Protein O-GlcNAcase X-ray 2.50 2023-05-10 74.75 0.94 0.04 ok
8DPU_A P40189 Interleukin-6 receptor subunit beta X-ray 3.78 2022-07-17 74.62 0.94 0.04 ok
8OX7_A O43520 Phospholipid-transporting ATPase IC EM 2.56 2023-05-01 80.38 0.94 0.04 ok
8JH3_c P04908 Histone H2A type 1-B/E EM 3.70 2023-05-22 90.75 0.95 0.04 ok
8OX9_A O43520 Phospholipid-transporting ATPase IC EM 2.72 2023-05-01 80.38 0.94 0.04 ok
8DPV_A P20809 Interleukin-11 X-ray 1.48 2022-07-17 82.62 0.95 0.04 ok
8DPS_B P20809 Interleukin-11 EM 3.47 2022-07-17 82.62 0.95 0.04 ok
8BPW_A O60674 Tyrosine-protein kinase JAK2 X-ray 1.80 2022-11-18 86.88 0.95 0.04 ok
8BPV_A O60674 Tyrosine-protein kinase JAK2 X-ray 1.70 2022-11-18 86.88 0.95 0.04 ok
8TYP_A P09871 Complement C1s subcomponent X-ray 1.80 2023-08-25 87.88 0.95 0.04 ok
8JH2_c P04908 Histone H2A type 1-B/E EM 5.70 2023-05-22 90.75 0.96 0.04 ok
8WZD_A P49773 Adenosine 5'-monophosphoramidase HINT1 X-ray 2.05 2023-11-01 96.19 0.96 0.04 ok
8JH4_c P04908 Histone H2A type 1-B/E EM 3.20 2023-05-22 90.75 0.96 0.03 ok
7YG5_A Q15878 Voltage-dependent R-type calcium channel s EM 3.00 2022-07-11 59.94 0.94 0.03 ok
7R0D_AAA Q9NV35 Probable 8-oxo-dGTP diphosphatase NUDT15 X-ray 1.70 2022-02-01 92.75 0.97 0.03 ok
7ZXB_A Q86WV6 Stimulator of interferon protein X-ray 3.00 2022-05-20 83.75 0.97 0.03 ok
7ZWL_A Q86WV6 Stimulator of interferon protein X-ray 2.00 2022-05-19 83.75 0.97 0.03 ok
8J6K_a P49662 Caspase-4 subunit p10 X-ray 3.12 2023-04-26 78.38 0.97 0.03 ok
7YG5_B Q02641 Voltage-dependent L-type calcium channel s EM 3.00 2022-07-11 69.00 0.96 0.03 ok
8WRL_A Q9BYF1 Processed angiotensin-converting enzyme 2 EM 3.36 2023-10-15 90.69 0.97 0.03 ok
8T5Q_A Q12933 TNF receptor-associated factor 2 X-ray 1.90 2023-06-14 90.19 0.97 0.03 ok
8WRH_A Q9BYF1 Angiotensin-converting enzyme 2 EM 3.08 2023-10-14 90.69 0.97 0.03 ok
8BPI_XXX P07320 Gamma-crystallin D X-ray 2.00 2022-11-16 96.44 0.97 0.03 ok
7ZVK_A Q86WV6 Stimulator of interferon protein X-ray 2.83 2022-05-16 83.75 0.97 0.03 ok
7XUZ_C Q02078 myocyte-specific enhancer factor 2A isofor X-ray 3.59 2022-05-20 54.72 0.96 0.02 ok
8OY2_A P24941 Cyclin-dependent kinase 2 X-ray 2.62 2023-05-03 88.44 0.98 0.02 ok
8JH2_b P62805 Histone H4 EM 5.70 2023-05-22 89.81 0.98 0.02 ok
8BOS_G P20936 Ras GTPase-activating protein 1 X-ray 2.10 2022-11-15 75.44 0.97 0.02 ok
8HNI_A P22626 Heterogeneous nuclear ribonucleoproteins A X-ray 2.64 2022-12-07 69.19 0.97 0.02 ok
7ZVF_A P07711 Cathepsin L X-ray 1.60 2022-05-15 93.50 0.98 0.02 ok
8OX6_A O43520 Phospholipid-transporting ATPase IC EM 2.39 2023-05-01 80.38 0.98 0.02 ok
8OFA_A P07711 Cathepsin L X-ray 1.90 2023-03-14 93.50 0.98 0.02 ok
8PVB_A P28472 Gamma-aminobutyric acid receptor subunit b EM 3.60 2023-07-17 80.06 0.98 0.02 ok
8F8M_A O00482 Nuclear receptor subfamily 5 group A membe X-ray 2.60 2022-11-22 72.12 0.98 0.02 ok
8JH3_d P06899 Histone H2B type 1-J EM 3.70 2023-05-22 85.50 0.98 0.02 ok
8JVL_A Q9NPD8 Ubiquitin-conjugating enzyme E2 T X-ray 2.06 2023-06-28 86.25 0.98 0.01 ok
8JVE_A Q9NPD8 Ubiquitin-conjugating enzyme E2 T X-ray 1.76 2023-06-28 86.25 0.98 0.01 ok
8BOS_R P01112 GTPase HRas X-ray 2.10 2022-11-15 91.94 0.98 0.01 ok
8JH3_a P84243 Histone H3.3 EM 3.70 2023-05-22 85.94 0.98 0.01 ok
8JH2_a P84243 Histone H3.3 EM 5.70 2023-05-22 85.94 0.98 0.01 ok
8F7L_A P43490 Nicotinamide phosphoribosyltransferase X-ray 2.20 2022-11-18 94.25 0.99 0.01 ok
8T5P_A Q13114 TNF receptor-associated factor 3 X-ray 2.50 2023-06-14 87.88 0.99 0.01 ok
8J6K_A P49662 Caspase-4 subunit p20 X-ray 3.12 2023-04-26 78.38 0.99 0.01 ok
8JH4_a P84243 Histone H3.3 EM 3.20 2023-05-22 85.94 0.99 0.01 ok
8JH4_d P06899 Histone H2B type 1-J EM 3.20 2023-05-22 85.50 0.99 0.01 ok
8T9U_F P17947 Transcription factor PU.1 X-ray 1.47 2023-06-26 65.50 0.99 0.01 ok
8ATB_AAA Q9NWZ3 Interleukin-1 receptor-associated kinase 4 X-ray 2.35 2022-08-22 83.94 0.99 0.01 ok
8F5X_A P10153 Non-secretory ribonuclease X-ray 1.70 2022-11-15 91.19 0.99 0.01 ok
8JH3_b P62805 Histone H4 EM 3.70 2023-05-22 89.81 0.99 0.01 ok
8JH4_b P62805 Histone H4 EM 3.20 2023-05-22 89.81 0.99 0.01 ok
8JH2_d P06899 Histone H2B type 1-J EM 5.70 2023-05-22 85.50 0.99 0.01 ok
8BPI_AAA P07320 Gamma-crystallin D X-ray 2.00 2022-11-16 96.44 0.99 0.01 ok
8K2X_B P62873 Guanine nucleotide-binding protein G(I)/G( EM 3.20 2023-07-14 97.06 0.99 0.01 ok
7YG5_D P54289 Voltage-dependent calcium channel subunit EM 3.00 2022-07-11 86.56 0.99 0.01 ok
8HNK_B P62873 Guanine nucleotide-binding protein G(I)/G( EM 3.01 2022-12-08 97.06 1.00 0.00 ok
8HNM_B P62873 Guanine nucleotide-binding protein G(I)/G( EM 2.94 2022-12-08 97.06 1.00 0.00 ok
8HNL_B P62873 Guanine nucleotide-binding protein G(I)/G( EM 2.98 2022-12-08 97.06 1.00 0.00 ok
8BOE_AAA P00918 Carbonic anhydrase 2 X-ray 1.55 2022-11-15 97.38 1.00 0.00 ok
8BOW_A Q04609 Glutamate carboxypeptidase 2 X-ray 1.58 2022-11-15 93.81 1.00 0.00 ok
8BOL_A Q04609 Glutamate carboxypeptidase 2 X-ray 1.55 2022-11-15 93.81 1.00 0.00 ok
8BO8_A Q04609 Glutamate carboxypeptidase 2 X-ray 1.55 2022-11-15 93.81 1.00 0.00 ok
8PVH_A P00352 Aldehyde dehydrogenase 1A1 EM 2.90 2023-07-17 97.81 1.00 0.00 ok
8PVD_A P04040 Catalase EM 3.40 2023-07-17 95.81 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.