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

Release week 2021-03-31

124
structures analysed (21 full · 16.9%)
54.0%
confidently wrong
32.4%
novel sequences
10.8%
novel & wrong
0.947
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: 5 of 124 structures (4.0%) are confidently wrong; median TM-score is 0.947.

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 0.947 — 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
7M4R_A Q8N3R9 MAGUK p55 subfamily member 5 EM 3.65 2021-03-22 0.30 91.73 0.59 0.79 2.85 20.78 0.81 ok
7DVQ_v Q9BWG6 Sodium channel modifier 1 EM 2.89 2021-01-14 100.00 novel 83.52 0.46 0.85 1.89 25.05 0.78 wrong
7K02_A Q16611 Bcl-2 homologous antagonist/killer X-ray 3.40 2020-09-02 0.00 86.57 0.53 0.81 5.71 19.34 0.71 ok
7DVQ_9 Q13356 RING-type E3 ubiquitin-protein ligase PPIL EM 2.89 2021-01-14 0.00 86.91 0.49 0.91 3.36 15.05 0.71 wrong
7DVQ_V Q9HCG8 Pre-mRNA-splicing factor CWC22 homolog EM 2.89 2021-01-14 0.00 89.74 0.61 0.96 8.33 11.17 0.59 ok
7DVQ_J Q9BZJ0 Crooked neck-like protein 1 EM 2.89 2021-01-14 0.00 88.30 0.67 0.56 14.89 12.64 0.54 ok
7DVQ_M O15541 RING finger protein 113A EM 2.89 2021-01-14 57.20 81.86 0.48 0.84 16.62 10.26 0.47 wrong
7DVQ_R Q13573 SNW domain-containing protein 1 EM 2.89 2021-01-14 0.00 83.33 0.62 0.87 16.29 9.73 0.44 ok
7BRJ_L P01160 Urodilatin X-ray 2.70 2020-03-29 0.00 60.16 0.20 0.51 27.27 6.79 0.24 ok
7BRH_L P01160 Natriuretic peptides A X-ray 2.45 2020-03-29 0.00 59.68 0.17 0.49 30.00 6.98 0.24 ok
6Y9H_L P00734 Prothrombin X-ray 1.48 2020-03-09 83.94 0.72 0.24 ok
6YB6_L P00734 Prothrombin X-ray 1.33 2020-03-16 83.94 0.72 0.23 ok
7DVQ_A Q6P2Q9 Pre-mRNA-processing-splicing factor 8 EM 2.89 2021-01-14 84.94 0.74 0.22 ok
7DVQ_5 Q9Y3B4 Splicing factor 3B subunit 6 EM 2.89 2021-01-14 90.12 0.75 0.22 ok
7DVQ_P Q9P013 Spliceosome-associated protein CWC15 homol EM 2.89 2021-01-14 74.88 0.71 0.22 ok
7BRK_L P01160 Natriuretic peptides A X-ray 2.85 2020-03-29 0.00 60.26 0.14 0.52 34.78 5.95 0.21 ok
7DVQ_0 Q9P021 Cysteine-rich PDZ-binding protein EM 2.89 2021-01-14 100.00 novel 78.67 0.66 0.70 42.00 5.24 0.21 ok
7DVQ_2 Q13435 Splicing factor 3B subunit 2 EM 2.89 2021-01-14 65.69 0.70 0.20 ok
7BP9_A P55072 Transitional endoplasmic reticulum ATPase EM 3.60 2020-03-21 82.56 0.79 0.18 ok
7BPA_A P55072 Transitional endoplasmic reticulum ATPase EM 3.30 2020-03-21 82.56 0.79 0.17 ok
7BP8_A P55072 Transitional endoplasmic reticulum ATPase EM 3.90 2020-03-21 82.56 0.79 0.17 ok
7DVQ_7 Q9BWJ5 Splicing factor 3B subunit 5 EM 2.89 2021-01-14 91.62 0.82 0.17 ok
7BPB_A P55072 Transitional endoplasmic reticulum ATPase EM 4.30 2020-03-22 82.56 0.80 0.17 ok
7DVQ_Z Q9BRD0 BUD13 homolog EM 2.89 2021-01-14 59.94 0.74 0.16 ok
7NE0_C Q6NW40 Repulsive Guidance Molecule B X-ray 3.25 2021-02-02 3.00 89.47 0.40 0.81 71.67 3.95 0.13 wrong
7NDG_M Q6NW40 RGM domain family member B EM 5.98 2021-02-01 2.50 89.47 0.40 0.81 71.67 3.95 0.13 wrong
7DVQ_1 O75533 Splicing factor 3B subunit 1 EM 2.89 2021-01-14 74.81 0.84 0.12 ok
7DVQ_K Q9H6L4 Armadillo repeat-containing protein 7 EM 2.89 2021-01-14 88.56 0.87 0.12 ok
7DVQ_4 Q15427 Splicing factor 3B subunit 4 EM 2.89 2021-01-14 73.19 0.86 0.10 ok
7DVQ_b P14678 Small nuclear ribonucleoprotein-associated EM 2.89 2021-01-14 69.50 0.86 0.10 ok
6WA2_A P00533 Epidermal growth factor receptor X-ray 2.40 2020-03-24 75.94 0.88 0.09 ok
7DVQ_y Q92917 G-patch domain and KOW motifs-containing p EM 2.89 2021-01-14 100.00 novel 56.09 0.34 0.77 53.85 2.56 0.09 ok
7KFZ_A P01116 GTPase KRas EM 3.47 2020-10-15 91.50 0.90 0.09 ok
6W5M_D Q9UBL3 Set1/Ash2 histone methyltransferase comple EM 4.60 2020-03-13 75.25 0.88 0.09 ok
6W5I_D Q9UBL3 Set1/Ash2 histone methyltransferase comple EM 6.90 2020-03-13 75.25 0.88 0.09 ok
6WAK_A P00533 Epidermal growth factor receptor X-ray 2.40 2020-03-25 75.94 0.89 0.09 ok
7D0E_B Q9ULG6 Cell cycle progression protein 1 FIR2 X-ray 1.40 2020-09-09 51.62 0.29 0.68 56.82 2.82 0.09 ok
6W5N_D Q9UBL3 Set1/Ash2 histone methyltransferase comple EM 6.00 2020-03-13 75.25 0.89 0.09 ok
7KFK_A Q8NHL6 Isoform 2 of Leukocyte immunoglobulin-like X-ray 2.63 2020-10-14 73.38 0.89 0.08 ok
7DVQ_Y Q9Y388 RNA-binding motif protein, X-linked 2 EM 2.89 2021-01-14 63.66 0.87 0.08 ok
7DVQ_d P62316 Small nuclear ribonucleoprotein Sm D2 EM 2.89 2021-01-14 90.62 0.91 0.08 ok
7DVQ_U Q9UQ35 Serine/arginine repetitive matrix protein EM 2.89 2021-01-14 0.00 81.26 0.52 0.83 78.85 2.07 0.08 ok
7DVQ_8 Q8IYB3 Serine/arginine repetitive matrix protein EM 2.89 2021-01-14 51.62 0.87 0.07 ok
7NE0_A O95631 Netrin-1 X-ray 3.25 2021-02-02 88.50 0.93 0.06 ok
6YB6_H P00734 Prothrombin X-ray 1.33 2020-03-16 83.94 0.92 0.06 ok
6Y9H_H P00734 Prothrombin X-ray 1.48 2020-03-09 83.94 0.92 0.06 ok
7DFL_R P35367 Histamine H1 receptor EM 3.30 2020-11-09 69.94 0.91 0.06 ok
7DVQ_x O60231 Pre-mRNA-splicing factor ATP-dependent RNA EM 2.89 2021-01-14 77.69 0.93 0.06 ok
6Y7J_A Q9H8M2 Bromodomain-containing protein 9 X-ray 1.60 2020-03-01 62.97 0.91 0.06 ok
6Y7K_A Q9H8M2 Bromodomain-containing protein 9 X-ray 1.20 2020-03-01 62.97 0.91 0.06 ok
7KFZ_B Q07889 Son of sevenless homolog 1 EM 3.47 2020-10-15 76.38 0.93 0.06 ok
7NDG_A O95631 Netrin-1 EM 5.98 2021-02-01 88.50 0.94 0.05 ok
6WQU_D Q9UM47 Neurogenic locus notch homolog protein 3 X-ray 2.41 2020-04-29 25.46 0.24 0.74 50.00 3.15 0.05 ok
6Y7I_A Q9H8M2 Bromodomain-containing protein 9 X-ray 1.60 2020-03-01 62.97 0.92 0.05 ok
7NE0_D Q6NW40 Repulsive Guidance Molecule B C-terminal r X-ray 3.25 2021-02-02 79.44 0.94 0.05 ok
6Y7H_A Q9H8M2 Bromodomain-containing protein 9 X-ray 1.80 2020-03-01 62.97 0.92 0.05 ok
7DWX_B Q9BYF1 Angiotensin-converting enzyme 2 EM 8.30 2021-01-18 90.69 0.95 0.05 ok
6Y7L_A Q9H8M2 Bromodomain-containing protein 9 X-ray 1.80 2020-03-01 62.97 0.92 0.05 ok
7JUP_A O75762 Transient receptor potential cation channe EM 3.05 2020-08-20 81.94 0.95 0.04 ok
7D0E_A Q8TDY2 RB1-inducible coiled-coil protein 1 X-ray 1.40 2020-09-09 72.50 0.94 0.04 ok
6Y7T_A P31947 14-3-3 protein sigma X-ray 2.50 2020-03-02 92.88 0.95 0.04 ok
6L71_A Q8IXJ6 NAD-dependent protein deacetylase sirtuin- X-ray 2.11 2019-10-30 0.00 92.82 0.98 0.96 95.27 1.00 0.04 ok
7DX9_D Q9BYF1 Angiotensin-converting enzyme 2 EM 3.60 2021-01-18 90.69 0.95 0.04 ok
7DX8_D Q9BYF1 Angiotensin-converting enzyme 2 EM 2.90 2021-01-18 90.69 0.95 0.04 ok
7DX7_D Q9BYF1 Angiotensin-converting enzyme 2 EM 3.40 2021-01-18 90.69 0.95 0.04 ok
7DX6_D Q9BYF1 Angiotensin-converting enzyme 2 EM 3.00 2021-01-18 90.69 0.95 0.04 ok
7DX5_D Q9BYF1 Angiotensin-converting enzyme 2 EM 3.30 2021-01-18 90.69 0.95 0.04 ok
7DVQ_g P62308 Small nuclear ribonucleoprotein G EM 2.89 2021-01-14 93.25 0.95 0.04 ok
7LO4_A Q9BYF1 Processed angiotensin-converting enzyme 2 X-ray 2.46 2021-02-09 90.69 0.95 0.04 ok
7DVQ_X Q8TAD8 Smad nuclear-interacting protein 1 EM 2.89 2021-01-14 66.06 0.94 0.04 ok
7DVQ_L Q99459 Cell division cycle 5-like protein EM 2.89 2021-01-14 74.31 0.94 0.04 ok
7DFL_G P59768 Guanine nucleotide-binding protein G(I)/G( EM 3.30 2020-11-09 89.56 0.96 0.04 ok
6L72_A Q8IXJ6 NAD-dependent protein deacetylase sirtuin- X-ray 2.50 2019-10-30 0.00 93.02 0.98 0.96 95.66 0.87 0.04 ok
7DVQ_I Q5RL73 RNA-binding protein 48 EM 2.89 2021-01-14 67.75 0.95 0.04 ok
7NDG_C Q6NW40 Repulsive Guidance Molecule B (C-terminal EM 5.98 2021-02-01 79.44 0.96 0.04 ok
6L23_A P68400 Casein kinase II subunit alpha X-ray 1.97 2019-10-02 0.30 97.00 0.99 0.96 96.11 0.91 0.03 ok
7DVQ_a P62318 Small nuclear ribonucleoprotein Sm D3 EM 2.89 2021-01-14 82.81 0.96 0.03 ok
6YDZ_A Q86WV6 Stimulator of interferon protein X-ray 2.90 2020-03-23 83.75 0.96 0.03 ok
6YE9_A P31947 14-3-3 protein sigma X-ray 1.80 2020-03-24 92.88 0.97 0.03 ok
7BEV_A Q07617 Sperm-associated antigen 1 NMR 2020-12-29 73.69 0.96 0.03 ok
6YDB_A Q86WV6 Stimulator of interferon protein X-ray 2.80 2020-03-20 83.75 0.97 0.03 ok
6Y99_A Q86WV6 Stimulator of interferon genes protein X-ray 2.98 2020-03-06 83.75 0.97 0.03 ok
7CZM_A Q8TDY2 RB1-inducible coiled-coil protein 1 X-ray 2.00 2020-09-09 72.50 0.96 0.03 ok
7CZG_A Q8TDY2 RB1-inducible coiled-coil protein 1 X-ray 1.80 2020-09-08 72.50 0.96 0.03 ok
6Y7G_A Q96E17 Ras-related protein Rab-3C X-ray 2.30 2020-02-29 82.62 0.97 0.03 ok
6YEA_A Q86WV6 Stimulator of interferon protein X-ray 2.81 2020-03-24 83.75 0.97 0.03 ok
7DVQ_e P62304 Small nuclear ribonucleoprotein E EM 2.89 2021-01-14 90.75 0.97 0.02 ok
6Y6R_A Q8N5J2 Ubiquitin carboxyl-terminal hydrolase MIND X-ray 3.32 2020-02-27 72.69 0.97 0.02 ok
7DVQ_f P62306 Small nuclear ribonucleoprotein F EM 2.89 2021-01-14 90.50 0.98 0.02 ok
7BPH_A P63092 Guanine nucleotide-binding protein G(s) su X-ray 1.57 2020-03-22 91.31 0.98 0.02 ok
7DWX_A Q695T7 Sodium-dependent neutral amino acid transp EM 8.30 2021-01-18 90.00 0.98 0.02 ok
7DVQ_C Q15029 116 kDa U5 small nuclear ribonucleoprotein EM 2.89 2021-01-14 89.94 0.98 0.02 ok
7NE1_A O95631 Netrin-1 X-ray 3.15 2021-02-02 88.50 0.98 0.02 ok
7D2V_A P56817 Beta-secretase 1 X-ray 2.10 2020-09-17 87.50 0.98 0.02 ok
6Y8P_A E5BBQ0 O6-alkylguanine-DNA alkyltransferase mutan X-ray 2.30 2020-03-05 90.50 0.98 0.02 ok
7DVQ_c P62314 Small nuclear ribonucleoprotein Sm D1 EM 2.89 2021-01-14 82.81 0.98 0.02 ok
7DVQ_3 Q15393 Splicing factor 3B subunit 3 EM 2.89 2021-01-14 92.25 0.98 0.02 ok
6W5I_A Q15291 Retinoblastoma-binding protein 5 EM 6.90 2020-03-13 77.75 0.98 0.02 ok
7DVQ_6 Q7RTV0 PHD finger-like domain-containing protein EM 2.89 2021-01-14 89.88 0.98 0.02 ok
6W5N_A Q15291 Retinoblastoma-binding protein 5 EM 6.00 2020-03-13 77.75 0.98 0.01 ok
6XIY_A Q8IUN9 C-type lectin domain family 10 member A X-ray 2.31 2020-06-22 80.44 0.98 0.01 ok
7DFL_B P62873 Guanine nucleotide-binding protein G(I)/G( EM 3.30 2020-11-09 97.06 0.99 0.01 ok
7DVQ_D O75643 U5 small nuclear ribonucleoprotein 200 kDa EM 2.89 2021-01-14 82.75 0.98 0.01 ok
7D2X_A P56817 Beta-secretase 1 X-ray 2.45 2020-09-17 87.50 0.99 0.01 ok
6W5M_A Q15291 Retinoblastoma-binding protein 5 EM 4.60 2020-03-13 77.75 0.99 0.01 ok
7D5U_A Q9Y5Z0 Beta-secretase 2 X-ray 2.04 2020-09-28 82.69 0.99 0.01 ok
7D5A_A P56817 Beta-secretase 1 X-ray 2.20 2020-09-25 87.50 0.99 0.01 ok
7LJ9_A P53396 ATP-citrate synthase EM 3.00 2021-01-28 92.25 0.99 0.01 ok
7DVQ_z Q6UX04 Peptidyl-prolyl cis-trans isomerase CWC27 EM 2.89 2021-01-14 73.56 0.99 0.01 ok
7E4T_A Q9UL62 Short transient receptor potential channel EM 3.00 2021-02-15 73.19 0.99 0.01 ok
7D4Q_A Q9UL62 Short transient receptor potential channel EM 2.74 2020-09-24 73.19 0.99 0.01 ok
7D4P_A Q9UL62 Short transient receptor potential channel EM 2.70 2020-09-24 73.19 0.99 0.01 ok
7JG0_A P22102 Trifunctional purine biosynthetic protein X-ray 1.98 2020-07-18 92.75 0.99 0.01 ok
6W5N_B P61964 WD repeat-containing protein 5 EM 6.00 2020-03-13 93.31 0.99 0.01 ok
6W5I_B P61964 WD repeat-containing protein 5 EM 6.90 2020-03-13 93.31 0.99 0.01 ok
6W5M_B P61964 WD repeat-containing protein 5 EM 4.60 2020-03-13 93.31 0.99 0.01 ok
7JG3_A P22102 Trifunctional purine biosynthetic protein X-ray 2.09 2020-07-18 92.75 0.99 0.01 ok
7D5B_A Q9Y5Z0 Beta-secretase 2 X-ray 1.31 2020-09-25 82.69 0.99 0.01 ok
7JG4_A P22102 Trifunctional purine biosynthetic protein X-ray 2.46 2020-07-18 92.75 0.99 0.01 ok
7DVQ_E Q96DI7 U5 small nuclear ribonucleoprotein 40 kDa EM 2.89 2021-01-14 85.25 0.99 0.01 ok
7EA9_A Q15046 Lysine--tRNA ligase X-ray 2.50 2021-03-06 90.50 0.99 0.01 ok
7DVQ_T O43660 Pleiotropic regulator 1 EM 2.89 2021-01-14 77.38 0.99 0.00 ok
6YRI_A P00918 Carbonic anhydrase 2 X-ray 1.60 2020-04-20 97.38 1.00 0.00 ok
6WVO_A P22303 Acetylcholinesterase X-ray 2.19 2020-05-06 92.94 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.