Single-chain structure prediction (PDB 2024)

protein

protein-ml/protein-structure-prediction Task: structure-prediction Visibility: PUBLIC

OverviewLeaderboard

Leaderboard

No results yet. When an evaluation of this benchmark is published, its ranked results will appear here, with their source and their uncertainty.

Protocol

What is measured. How close a model's predicted structure of a single protein chain is to the crystal structure of that chain, from the sequence alone.

Pool. One RCSB search, frozen with its full answer (rcsb_chains.json): X-ray diffraction, resolution ≤ 2.5 Å, initial release between 2024-01-01 and 2024-12-31, exactly one protein polymer entity with exactly one deposited instance, entity sequence length 50-300, and only the representatives of 30 % sequence-identity clusters. That is 1,452 entities, 444 cluster representatives.

Items. The representatives in seed-hash order (seed 20261006), the first 100 that pass a quality check: the chain parses, its canonical sequence has only standard residue letters, and all four backbone atoms (N, CA, C, O) are observed at ≥ 80 % of positions. Eight were rejected (six for backbone completeness, one for an X in the sequence, one for both), and are listed with their reason in the frozen file. The 100 chains run 56-298 residues (median 196) at 1.00-2.48 Å.

Data. Each chain's mmCIF comes from the wwPDB versioned archive (files-versioned.wwpdb.org/.../pdb_0000xxxx_xyz_v<major>-<minor>.cif.gz) at the revision current when the benchmark was frozen, pinned by sha256: a versioned file never changes, so a later remediation of an entry cannot move the reference silently (it would be a new definition_version). Residue i of an item is position i of the entity's canonical sequence (_entity_poly.pdbx_seq_one_letter_code_can), tied to atoms through label_seq_id; the first model and the first alternate location are read.

Protocol. Zero-shot only (generate.structure). The worker gets item_id and sequence (the full deposited sequence, unobserved termini included) and writes one PDB or mmCIF per item; the predicted chain must have exactly as many residues as the sequence. Residue i of the prediction is compared with residue i of the crystal — a fixed correspondence, no alignment — on the positions whose Cα is observed (label_ca_mask). No MSA, template or structure database is provided by the harness; a model that uses them does so through its own adapter, and that is part of what the number measures.

Metrics. lDDT-Cα, TM-score (position correspondence, normalised by the number of evaluated reference residues) and Cα RMSD, each computed per chain and averaged over the 100 chains; 95 % bootstrap interval, 1,000 resamples of chains. Secondary: CASP's GDT-TS and GDT-HA on the Cα traces (gdt_ts_zero_shot, gdt_ha_zero_shot, as fractions, from the harness's own superposition search, a lower bound on LGA's), and CAMEO's all-atom lDDT (lddt_zero_shot) over every crystal heavy atom paired with the prediction's atom of the same residue and name, which the evaluator keeps in the frame. lDDT-Cα stays the headline: it is a defined variant and its label says so.

Caveats. A 2024 release date puts these entries after the training cutoff of AlphaFold2 (2018), ESMFold (2020) and most released folding models, but not after every model's: a model trained on a 2024+ PDB snapshot has seen them, which the export's overlap flag cannot detect (protein-ml/protein-data-bank is declared as a whole, not by date). 30 % identity clustering removes near-duplicates inside the pool but not homology to older PDB entries a model was trained on, which is the usual reason single-chain prediction looks easy. Crystal structures carry crystallisation artefacts (termini, crystal contacts) that a predictor is scored against; lDDT and TM-score are the robust numbers here, RMSD the fragile one. Monomers only: no complex, no ligand, no multi-chain assembly.

Data

rcsb: api_frozen ?, licence search answer (RCSB data are CC0-1.0), catalogued as protein-ml/protein-data-bank
pdb-7hll: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/hl/pdb_00007hll/pdb_00007hll_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8bp1: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/bp/pdb_00008bp1/pdb_00008bp1_xyz_v1-3.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8cd5: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/cd/pdb_00008cd5/pdb_00008cd5_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8cmp: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/cm/pdb_00008cmp/pdb_00008cmp_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8cpq: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/cp/pdb_00008cpq/pdb_00008cpq_xyz_v1-2.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8gc6: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/gc/pdb_00008gc6/pdb_00008gc6_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8gi6: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/gi/pdb_00008gi6/pdb_00008gi6_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8hy9: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/hy/pdb_00008hy9/pdb_00008hy9_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8ii8: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/ii/pdb_00008ii8/pdb_00008ii8_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8is9: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/is/pdb_00008is9/pdb_00008is9_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8izt: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/iz/pdb_00008izt/pdb_00008izt_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8j5h: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/j5/pdb_00008j5h/pdb_00008j5h_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8j5i: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/j5/pdb_00008j5i/pdb_00008j5i_xyz_v1-2.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8j7q: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/j7/pdb_00008j7q/pdb_00008j7q_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8jnb: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/jn/pdb_00008jnb/pdb_00008jnb_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8jqu: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/jq/pdb_00008jqu/pdb_00008jqu_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8k4m: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/k4/pdb_00008k4m/pdb_00008k4m_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8k8f: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/k8/pdb_00008k8f/pdb_00008k8f_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8ka7: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/ka/pdb_00008ka7/pdb_00008ka7_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8kac: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/ka/pdb_00008kac/pdb_00008kac_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8kb6: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/kb/pdb_00008kb6/pdb_00008kb6_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8kc4: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/kc/pdb_00008kc4/pdb_00008kc4_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8kg4: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/kg/pdb_00008kg4/pdb_00008kg4_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8okq: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/ok/pdb_00008okq/pdb_00008okq_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8omi: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/om/pdb_00008omi/pdb_00008omi_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8ovq: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/ov/pdb_00008ovq/pdb_00008ovq_xyz_v1-2.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8oxd: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/ox/pdb_00008oxd/pdb_00008oxd_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8oxr: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/ox/pdb_00008oxr/pdb_00008oxr_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8peb: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/pe/pdb_00008peb/pdb_00008peb_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8pjx: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/pj/pdb_00008pjx/pdb_00008pjx_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8pkb: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/pk/pdb_00008pkb/pdb_00008pkb_xyz_v1-2.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8pnx: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/pn/pdb_00008pnx/pdb_00008pnx_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8por: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/po/pdb_00008por/pdb_00008por_xyz_v1-2.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8prr: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/pr/pdb_00008prr/pdb_00008prr_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8pvq: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/pv/pdb_00008pvq/pdb_00008pvq_xyz_v1-2.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8q1v: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/q1/pdb_00008q1v/pdb_00008q1v_xyz_v2-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8qaz: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/qa/pdb_00008qaz/pdb_00008qaz_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8qdj: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/qd/pdb_00008qdj/pdb_00008qdj_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8qp7: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/qp/pdb_00008qp7/pdb_00008qp7_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8qua: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/qu/pdb_00008qua/pdb_00008qua_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8qup: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/qu/pdb_00008qup/pdb_00008qup_xyz_v1-2.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8qzh: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/qz/pdb_00008qzh/pdb_00008qzh_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8r39: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/r3/pdb_00008r39/pdb_00008r39_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8r5l: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/r5/pdb_00008r5l/pdb_00008r5l_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8r8o: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/r8/pdb_00008r8o/pdb_00008r8o_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8r9r: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/r9/pdb_00008r9r/pdb_00008r9r_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8rcy: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/rc/pdb_00008rcy/pdb_00008rcy_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8rij: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/ri/pdb_00008rij/pdb_00008rij_xyz_v1-2.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8rom: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/ro/pdb_00008rom/pdb_00008rom_xyz_v1-3.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8rqy: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/rq/pdb_00008rqy/pdb_00008rqy_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8sif: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/si/pdb_00008sif/pdb_00008sif_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8slr: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/sl/pdb_00008slr/pdb_00008slr_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8snq: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/sn/pdb_00008snq/pdb_00008snq_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8t2m: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/t2/pdb_00008t2m/pdb_00008t2m_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8t5a: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/t5/pdb_00008t5a/pdb_00008t5a_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8tat: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/ta/pdb_00008tat/pdb_00008tat_xyz_v2-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8tav: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/ta/pdb_00008tav/pdb_00008tav_xyz_v1-2.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8tct: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/tc/pdb_00008tct/pdb_00008tct_xyz_v1-2.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8tqg: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/tq/pdb_00008tqg/pdb_00008tqg_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8twn: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/tw/pdb_00008twn/pdb_00008twn_xyz_v1-4.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8u57: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/u5/pdb_00008u57/pdb_00008u57_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8uan: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/ua/pdb_00008uan/pdb_00008uan_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8uds: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/ud/pdb_00008uds/pdb_00008uds_xyz_v1-3.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8upb: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/up/pdb_00008upb/pdb_00008upb_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8uss: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/us/pdb_00008uss/pdb_00008uss_xyz_v1-3.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8vrg: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/vr/pdb_00008vrg/pdb_00008vrg_xyz_v1-3.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8w13: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/w1/pdb_00008w13/pdb_00008w13_xyz_v1-3.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8w1d: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/w1/pdb_00008w1d/pdb_00008w1d_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8w4b: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/w4/pdb_00008w4b/pdb_00008w4b_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8w4m: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/w4/pdb_00008w4m/pdb_00008w4m_xyz_v1-2.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8wcj: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/wc/pdb_00008wcj/pdb_00008wcj_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8wsv: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/ws/pdb_00008wsv/pdb_00008wsv_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8xe7: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/xe/pdb_00008xe7/pdb_00008xe7_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8y8y: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/y8/pdb_00008y8y/pdb_00008y8y_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8yhv: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/yh/pdb_00008yhv/pdb_00008yhv_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8zj9: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/zj/pdb_00008zj9/pdb_00008zj9_xyz_v2-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8zmn: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/zm/pdb_00008zmn/pdb_00008zmn_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8zqf: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/zq/pdb_00008zqf/pdb_00008zqf_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-8zxq: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/zx/pdb_00008zxq/pdb_00008zxq_xyz_v1-2.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9b3n: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/b3/pdb_00009b3n/pdb_00009b3n_xyz_v1-2.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9bjw: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/bj/pdb_00009bjw/pdb_00009bjw_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9bka: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/bk/pdb_00009bka/pdb_00009bka_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9bkf: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/bk/pdb_00009bkf/pdb_00009bkf_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9c8l: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/c8/pdb_00009c8l/pdb_00009c8l_xyz_v1-2.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9ce4: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/ce/pdb_00009ce4/pdb_00009ce4_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9cj0: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/cj/pdb_00009cj0/pdb_00009cj0_xyz_v1-4.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9ctx: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/ct/pdb_00009ctx/pdb_00009ctx_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9deu: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/de/pdb_00009deu/pdb_00009deu_xyz_v1-2.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9dug: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/du/pdb_00009dug/pdb_00009dug_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9e7c: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/e7/pdb_00009e7c/pdb_00009e7c_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9e9m: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/e9/pdb_00009e9m/pdb_00009e9m_xyz_v1-3.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9eat: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/ea/pdb_00009eat/pdb_00009eat_xyz_v1-2.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9f7j: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/f7/pdb_00009f7j/pdb_00009f7j_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9f96: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/f9/pdb_00009f96/pdb_00009f96_xyz_v1-2.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9fsa: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/fs/pdb_00009fsa/pdb_00009fsa_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9fse: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/fs/pdb_00009fse/pdb_00009fse_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9ghy: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/gh/pdb_00009ghy/pdb_00009ghy_xyz_v1-1.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9h48: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/h4/pdb_00009h48/pdb_00009h48_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9kbt: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/kb/pdb_00009kbt/pdb_00009kbt_xyz_v1-2.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank
pdb-9mgj: url https://files-versioned.wwpdb.org/pdb_versioned/data/entries/mg/pdb_00009mgj/pdb_00009mgj_xyz_v1-0.cif.gz, licence CC0-1.0, catalogued as protein-ml/protein-data-bank

Subset

seed 20261006
test: 100 item(s)
train: all item(s)

Metrics

lddt_ca_zero_shot — lDDT-Cα; protocol zero_shot; higher is better; range [0.0, 1.0]; 95% bootstrap CI, 1000 resamples
tm_score_zero_shot — TM-score; protocol zero_shot; higher is better; range [0.0, 1.0]; 95% bootstrap CI, 1000 resamples
rmsd_ca_zero_shot — Cα RMSD, Å; protocol zero_shot; lower is better; range ≥ 0.0; 95% bootstrap CI, 1000 resamples
gdt_ts_zero_shot — GDT-TS (Cα); protocol zero_shot; higher is better; range [0.0, 1.0]; 95% bootstrap CI, 1000 resamples
gdt_ha_zero_shot — GDT-HA (Cα); protocol zero_shot; higher is better; range [0.0, 1.0]; 95% bootstrap CI, 1000 resamples
lddt_zero_shot — lDDT (all heavy atoms); protocol zero_shot; higher is better; range [0.0, 1.0]; 95% bootstrap CI, 1000 resamples

Sample

Three of the 100 chains (input: the deposited sequence; expected output: a structure of that many residues, scored against the crystal Cα trace):

item_id	residues	observed Cα	resolution	released	mmCIF version
`7HLL_A`	188	185	1.15 Å	2024-11-27	v1.0
`8CMP_A`	66	58	1.06 Å	2024-03-06	v1.1
`8BP1_A`	242	231	1.72 Å	2024-02-28	v1.3

8CMP_A starts GHMAEVLVVTSKVKKLIKEKGQMNTSAETIDVLSKAIEQL… (66 residues, an expression tag included, as deposited). 58 of its positions have an observed Cα, so lDDT, TM-score and RMSD are computed on those 58. A perfect prediction scores lDDT-Cα 1.0, TM-score 1.0 and RMSD 0 Å; a prediction with the right fold but shifted loops typically lands near lDDT 0.8, TM-score 0.9 and RMSD 1-2 Å.