Release week 2021-07-14

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109

structures analysed (7 full · 6.4%)

10.9%

confidently wrong

00.0%

novel sequences

00.0%

novel & wrong

0.96

median TM-score

⭐ This week's notable releases

0 novel sequences, 1 confidently wrong. Highlight: THR-LEU-TYR-TYR-MET-ALA-PRO-GLU-HIS-LEU-ASN-ASP-.

PDB	Protein	Flags	Why it matters
7CJB_D ↗	THR-LEU-TYR-TYR-MET-ALA-PRO-GLU-HIS-LEU-ASN-ASP-	confidently wrong	A close pre-cutoff homolog existed yet AlphaFold confidently missed the fold.

see all 109 structures ↓

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: 1 of 109 structures (0.9%) are confidently wrong; median TM-score is 0.96.

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 0.96 — 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

PDB	UniProt	Protein	Method	Å	Deposited	Novelty %	pLDDT	TM	lDDT	GDT_TS	RMSD	FRAUD	Flag
7LB1_A	P21675	Transcription initiation factor TFIID subu	X-ray	1.35	2021-01-07	0.00	89.54	0.55	0.90	3.61	16.55	0.72	ok
7LB2_A	P21675	Transcription initiation factor TFIID subu	X-ray	1.70	2021-01-07	0.00	89.60	0.54	0.90	3.74	16.51	0.72	ok
7LB0_A	P21675	Transcription initiation factor TFIID subu	X-ray	2.33	2021-01-07	0.00	89.54	0.55	0.90	3.53	16.50	0.72	ok
7OKY_Z	O00267	Transcription elongation factor SPT5	EM	4.14	2021-05-18	0.00	90.27	0.64	0.88	11.16	13.70	0.58	ok
7EPU_B	Q86WJ1	Chromodomain-helicase-DNA-binding protein	X-ray	3.50	2021-04-27	55.20	79.15	0.63	0.72	15.51	11.91	0.48	ok
7D4B_A	Q07011	Tumor necrosis factor receptor superfamily	X-ray	3.14	2020-09-23	35.80	94.01	0.68	0.92	38.67	6.27	0.30	ok
7CJB_D	Q13546	THR-LEU-TYR-TYR-MET-ALA-PRO-GLU-HIS-LEU-AS	X-ray	2.80	2020-07-09	—	92.88	0.39	0.61	50.00	4.06	0.21	wrong
7F1Q_A	P63096	Guanine nucleotide-binding protein G(i) su	EM	2.90	2021-06-09	—	93.75	0.81	—	—	—	0.18	ok
7F1R_A	P63096	Guanine nucleotide-binding protein G(i) su	EM	3.00	2021-06-09	—	93.75	0.82	—	—	—	0.17	ok
7F1S_A	P63096	Guanine nucleotide-binding protein G(i) su	EM	2.80	2021-06-09	—	93.75	0.82	—	—	—	0.16	ok
7OKY_M	O00472	RNA polymerase II elongation factor ELL2	EM	4.14	2021-05-18	—	65.62	0.76	—	—	—	0.16	ok
7OKX_M	O00472	RNA polymerase II elongation factor ELL2	EM	3.30	2021-05-18	—	65.62	0.76	—	—	—	0.16	ok
7DUQ_R	P43220	Glucagon-like peptide 1 receptor	EM	2.50	2021-01-11	—	81.50	0.81	—	—	—	0.16	ok
7DRT_A	P56704	Protein Wnt-3a	EM	2.20	2020-12-29	—	88.31	0.82	—	—	—	0.16	ok
7DUQ_P	P01275	Glucagon-like peptide 1	EM	2.50	2021-01-11	—	68.94	0.79	—	—	—	0.14	ok
7DUQ_A	P63092	Guanine nucleotide-binding protein G(s) su	EM	2.50	2021-01-11	—	91.31	0.86	—	—	—	0.13	ok
7F1Q_C	P59768	Guanine nucleotide-binding protein G(I)/G(	EM	2.90	2021-06-09	—	89.56	0.87	—	—	—	0.12	ok
7LJ1_A	Q06830	Peroxiredoxin-1	X-ray	2.97	2021-01-28	—	97.19	0.88	—	—	—	0.11	ok
7F1S_C	P59768	Guanine nucleotide-binding protein G(I)/G(	EM	2.80	2021-06-09	—	89.56	0.89	—	—	—	0.10	ok
7F1R_C	P59768	Guanine nucleotide-binding protein G(I)/G(	EM	3.00	2021-06-09	—	89.56	0.89	—	—	—	0.10	ok
6XCP_C	O19707	Hybrid insulin peptide, MHC class II HLA-D	X-ray	3.30	2020-06-08	—	89.31	0.89	—	—	—	0.10	ok
6XCO_B	O19707	Hybrid Insulin Peptide, MHC class II HLA-D	X-ray	2.90	2020-06-08	—	89.31	0.89	—	—	—	0.09	ok
7F1S_R	P51681	C-C chemokine receptor type 5	EM	2.80	2021-06-09	—	85.38	0.89	—	—	—	0.09	ok
6XC9_C	O19707	Hybrid Insulin Peptide, MHC class II HLA-D	X-ray	2.40	2020-06-08	—	89.31	0.90	—	—	—	0.09	ok
7ENN_K	Q86WJ1	Chromodomain-helicase-DNA-binding protein	EM	2.80	2021-04-18	—	73.19	0.88	—	—	—	0.09	ok
7DRT_B	Q5T9L3	Protein wntless homolog	EM	2.20	2020-12-29	—	82.56	0.90	—	—	—	0.08	ok
7OKX_O	Q96JC9	ELL-associated factor 1	EM	3.30	2021-05-18	—	70.75	0.89	—	—	—	0.08	ok
7OKY_O	Q96JC9	ELL-associated factor 1	EM	4.14	2021-05-18	—	70.75	0.89	—	—	—	0.08	ok
7LEJ_A	Q58F21	Bromodomain testis-specific protein	X-ray	1.73	2021-01-14	—	62.44	0.88	—	—	—	0.07	ok
7EP2_A	Q9C0D3	Protein zyg-11 homolog B	X-ray	2.38	2021-04-26	—	92.31	0.93	—	—	—	0.06	ok
7E25_A	O15540	Fatty acid-binding protein, brain	X-ray	1.60	2021-02-04	—	96.31	0.94	—	—	—	0.06	ok
7E7E_A	Q9BYF1	Processed angiotensin-converting enzyme 2	X-ray	3.80	2021-02-26	—	90.69	0.94	—	—	—	0.06	ok
7EA8_C	P20671	Histone H2A type 1-D	EM	3.10	2021-03-06	—	90.94	0.94	—	—	—	0.06	ok
7BV7_C	Q9UL03	Integrator complex subunit 6	X-ray	2.40	2020-04-09	—	72.50	0.92	—	—	—	0.06	ok
7LW7_A	Q9H790	Exonuclease V	X-ray	2.50	2021-02-27	—	80.00	0.94	—	—	—	0.05	ok
7EP5_A	Q7Z7L7	Protein zer-1 homolog	X-ray	2.02	2021-04-26	—	90.81	0.94	—	—	—	0.05	ok
7EA8_A	Q6PI79	Histone H3.3	EM	3.10	2021-03-06	—	85.81	0.95	—	—	—	0.05	ok
7LJ1_a	Q9BYN0	Sulfiredoxin-1	X-ray	2.97	2021-01-28	—	83.69	0.95	—	—	—	0.05	ok
6XQ8_A	Q15109	Advanced glycosylation end product-specifi	X-ray	1.82	2020-07-09	—	82.81	0.95	—	—	—	0.04	ok
7EP1_A	Q9C0D3	Protein zyg-11 homolog B	X-ray	1.85	2021-04-26	—	92.31	0.95	—	—	—	0.04	ok
7EA8_L	Q9BYW2	Histone-lysine N-methyltransferase SETD2	EM	3.10	2021-03-06	—	43.34	0.90	—	—	—	0.04	ok
7OL0_Z	O00267	Transcription elongation factor SPT5	EM	3.00	2021-05-18	—	68.56	0.94	—	—	—	0.04	ok
7CJX_A	P54855	UDP-glucuronosyltransferase 2B15	X-ray	1.99	2020-07-14	—	93.38	0.95	—	—	—	0.04	ok
7P1L_A	P27448	MAP/microtubule affinity-regulating kinase	X-ray	1.95	2021-07-01	—	68.25	0.94	—	—	—	0.04	ok
6XQ9_A	Q15109	Advanced glycosylation end product-specifi	X-ray	2.30	2020-07-09	—	82.81	0.96	—	—	—	0.04	ok
6XQ6_A	Q15109	Advanced glycosylation end product-specifi	X-ray	1.90	2020-07-09	—	82.81	0.96	—	—	—	0.04	ok
7DCU_A	Q03933	Heat shock factor protein 2	X-ray	1.75	2020-10-27	—	59.47	0.94	—	—	—	0.03	ok
6XQ3_A	Q15109	Advanced glycosylation end product-specifi	X-ray	1.71	2020-07-09	—	82.81	0.96	—	—	—	0.03	ok
7KMF_J	Q9NR50	Translation initiation factor eIF-2B subun	EM	2.91	2020-11-02	—	72.56	0.95	—	—	—	0.03	ok
6XQ5_A	Q15109	Advanced glycosylation end product-specifi	X-ray	1.80	2020-07-09	—	82.81	0.96	—	—	—	0.03	ok
7EP0_A	Q9C0D3	Protein zyg-11 homolog B	X-ray	2.16	2021-04-26	—	92.31	0.96	—	—	—	0.03	ok
6ZLX_A	Q9Y2S7	Polymerase delta-interacting protein 2	X-ray	3.39	2020-07-01	—	79.75	0.96	—	—	—	0.03	ok
6XQ1_A	Q15109	Advanced glycosylation end product-specifi	X-ray	1.51	2020-07-09	—	82.81	0.96	—	—	—	0.03	ok
6XQ7_A	Q15109	Advanced glycosylation end product-specifi	X-ray	1.80	2020-07-09	—	82.81	0.96	—	—	—	0.03	ok
7LEL_A	Q58F21	Bromodomain testis-specific protein	X-ray	2.15	2021-01-14	—	62.44	0.95	—	—	—	0.03	ok
7OKX_Z	O00267	Transcription elongation factor SPT5	EM	3.30	2021-05-18	—	68.56	0.95	—	—	—	0.03	ok
7LEK_A	Q58F21	Bromodomain testis-specific protein	X-ray	2.75	2021-01-14	—	62.44	0.95	—	—	—	0.03	ok
7LAK_A	P25440	Bromodomain-containing protein 2	X-ray	1.83	2021-01-06	—	64.06	0.95	—	—	—	0.03	ok
6XCP_A	Q30069	MHC class II HLA-DQ-alpha chain	X-ray	3.30	2020-06-08	—	91.56	0.97	—	—	—	0.03	ok
7JYQ_A	O60674	Tyrosine-protein kinase JAK2	X-ray	1.86	2020-08-31	—	86.88	0.97	—	—	—	0.03	ok
7JYO_A	O60674	Tyrosine-protein kinase JAK2	X-ray	2.16	2020-08-31	—	86.88	0.97	—	—	—	0.03	ok
7LWA_A	Q9H790	Exonuclease V	X-ray	2.85	2021-02-28	—	80.00	0.97	—	—	—	0.03	ok
6XS5_A	Q9UBQ0	Vacuolar protein sorting-associated protei	X-ray	2.01	2020-07-15	—	96.62	0.98	—	—	—	0.02	ok
7LBT_A	Q15059	Bromodomain-containing protein 3	X-ray	2.70	2021-01-08	—	66.88	0.97	—	—	—	0.02	ok
7KMF_C	P49770	Translation initiation factor eIF-2B subun	EM	2.91	2020-11-02	—	86.56	0.97	—	—	—	0.02	ok
7MEZ_A	P48736	Phosphatidylinositol 4,5-bisphosphate 3-ki	EM	2.89	2021-04-08	—	87.81	0.98	—	—	—	0.02	ok
7CJB_C	Q15369	Elongin-C	X-ray	2.80	2020-07-09	—	89.81	0.98	—	—	—	0.02	ok
7EA8_D	P06899	Histone H2B type 2-E	EM	3.10	2021-03-06	—	85.50	0.98	—	—	—	0.02	ok
7LW8_A	Q9H790	Exonuclease V	X-ray	2.88	2021-02-28	—	80.00	0.97	—	—	—	0.02	ok
7OKY_Y	P63272	Transcription elongation factor SPT4	EM	4.14	2021-05-18	—	96.50	0.98	—	—	—	0.02	ok
7EA8_B	P62799	Histone H4	EM	3.10	2021-03-06	—	89.44	0.98	—	—	—	0.02	ok
7LAY_A	Q15059	Bromodomain-containing protein 3	X-ray	1.45	2021-01-07	—	66.88	0.97	—	—	—	0.02	ok
7EP4_A	Q7Z7L7	Protein zer-1 homolog	X-ray	2.07	2021-04-26	—	90.81	0.98	—	—	—	0.02	ok
7CZD_B	Q9NZQ7	Programmed cell death 1 ligand 1	X-ray	1.64	2020-09-08	—	88.25	0.98	—	—	—	0.02	ok
7LW9_A	Q9H790	Exonuclease V	X-ray	2.71	2021-02-28	—	80.00	0.98	—	—	—	0.02	ok
6XS7_A	Q9UBQ0	Vacuolar protein sorting-associated protei	X-ray	1.58	2020-07-15	—	96.62	0.98	—	—	—	0.02	ok
7EP3_A	Q7Z7L7	Protein zer-1 homolog	X-ray	1.51	2021-04-26	—	90.81	0.98	—	—	—	0.02	ok
7KMF_G	Q14232	Translation initiation factor eIF-2B subun	EM	2.91	2020-11-02	—	91.81	0.98	—	—	—	0.02	ok
6XCO_A	Q30069	MHC class II HLA-DQ-alpha chain	X-ray	2.90	2020-06-08	—	91.56	0.98	—	—	—	0.02	ok
7DCJ_A	Q00613	Heat shock factor protein 1	X-ray	2.00	2020-10-26	—	61.31	0.97	—	—	—	0.02	ok
7DZD_U	P00749	Urokinase-type plasminogen activator	X-ray	2.00	2021-01-25	—	82.12	0.98	—	—	—	0.02	ok
7KMF_E	Q9UI10	Translation initiation factor eIF-2B subun	EM	2.91	2020-11-02	—	76.50	0.98	—	—	—	0.02	ok
7CJB_B	Q15370	Elongin-B	X-ray	2.80	2020-07-09	—	92.50	0.98	—	—	—	0.02	ok
6XC9_A	Q30069	MHC class II HLA-DQ-alpha chain	X-ray	2.40	2020-06-08	—	91.56	0.98	—	—	—	0.01	ok
7M2N_A	P00338	L-lactate dehydrogenase A chain	X-ray	2.50	2021-03-17	—	96.19	0.99	—	—	—	0.01	ok
7KMF_B	Q13144	Translation initiation factor eIF-2B subun	EM	2.91	2020-11-02	—	78.75	0.98	—	—	—	0.01	ok
6XSA_A	Q9UBQ0	Vacuolar protein sorting-associated protei	X-ray	1.83	2020-07-15	—	96.62	0.99	—	—	—	0.01	ok
7LAZ_A	Q15059	Bromodomain-containing protein 3	X-ray	2.30	2021-01-07	—	66.88	0.98	—	—	—	0.01	ok
7LEM_A	Q58F21	Bromodomain testis-specific protein	X-ray	1.89	2021-01-14	—	62.44	0.98	—	—	—	0.01	ok
7DCI_A	Q03933	Heat shock factor protein 2	X-ray	1.70	2020-10-26	—	59.47	0.98	—	—	—	0.01	ok
7F1R_B	P62873	Guanine nucleotide-binding protein G(I)/G(	EM	3.00	2021-06-09	—	97.06	0.99	—	—	—	0.01	ok
7F1Q_B	P62873	Guanine nucleotide-binding protein G(I)/G(	EM	2.90	2021-06-09	—	97.06	0.99	—	—	—	0.01	ok
7BV7_A	Q68E01	Integrator complex subunit 3	X-ray	2.40	2020-04-09	—	83.06	0.99	—	—	—	0.01	ok
7F1S_B	P62873	Guanine nucleotide-binding protein G(I)/G(	EM	2.80	2021-06-09	—	97.06	0.99	—	—	—	0.01	ok
7M2O_A	Q9UJM8	Hydroxyacid oxidase 1	X-ray	2.07	2021-03-17	—	94.56	0.99	—	—	—	0.01	ok
7LB4_A	Q15059	Bromodomain-containing protein 3	X-ray	2.00	2021-01-07	—	66.88	0.99	—	—	—	0.01	ok
7DCT_A	Q00613	Heat shock factor protein 1	X-ray	2.36	2020-10-27	—	61.31	0.99	—	—	—	0.01	ok
7DCS_A	Q00613	Heat shock factor protein 1	X-ray	2.40	2020-10-27	—	61.31	0.99	—	—	—	0.01	ok
7OBP_A	Q8NI08	NCOA7-AS	X-ray	1.80	2021-04-23	—	55.62	0.99	—	—	—	0.01	ok
7OZ7_A	Q6V1X1	Dipeptidyl peptidase 8	X-ray	2.60	2021-06-26	—	90.44	0.99	—	—	—	0.01	ok
7CJ2_A	P36222	Chitinase 3-like 1 (Cartilage glycoprotein	X-ray	2.70	2020-07-09	—	94.69	0.99	—	—	—	0.01	ok
7CJB_A	P40337	von Hippel-Lindau disease tumor suppressor	X-ray	2.80	2020-07-09	—	84.44	0.99	—	—	—	0.01	ok
7NC4_A	P43166	Carbonic anhydrase 7	X-ray	1.60	2021-01-28	—	97.00	1.00	—	—	—	0.00	ok
7MYR_A	P56817	Beta-secretase 1	X-ray	1.72	2021-05-21	—	87.50	1.00	—	—	—	0.00	ok
7MOT_A	Q92769	Histone deacetylase 2	X-ray	1.54	2021-05-03	—	85.56	1.00	—	—	—	0.00	ok
7MOZ_A	Q92769	Histone deacetylase 2	X-ray	1.54	2021-05-03	—	85.56	1.00	—	—	—	0.00	ok
7MOY_A	Q92769	Histone deacetylase 2	X-ray	1.78	2021-05-03	—	85.56	1.00	—	—	—	0.00	ok
7MOX_A	Q92769	Histone deacetylase 2	X-ray	1.69	2021-05-03	—	85.56	1.00	—	—	—	0.00	ok
7MOS_A	Q92769	Histone deacetylase 2	X-ray	1.70	2021-05-03	—	85.56	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.