https://w3id.org/np/RA6ybgDshSUfsdNR6NqNuwKHseUV-MP1Fd6A1FzxepgTY/Head https://w3id.org/np/RA6ybgDshSUfsdNR6NqNuwKHseUV-MP1Fd6A1FzxepgTY http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RA6ybgDshSUfsdNR6NqNuwKHseUV-MP1Fd6A1FzxepgTY/assertion https://w3id.org/np/RA6ybgDshSUfsdNR6NqNuwKHseUV-MP1Fd6A1FzxepgTY http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RA6ybgDshSUfsdNR6NqNuwKHseUV-MP1Fd6A1FzxepgTY/provenance https://w3id.org/np/RA6ybgDshSUfsdNR6NqNuwKHseUV-MP1Fd6A1FzxepgTY http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RA6ybgDshSUfsdNR6NqNuwKHseUV-MP1Fd6A1FzxepgTY/pubinfo https://w3id.org/np/RA6ybgDshSUfsdNR6NqNuwKHseUV-MP1Fd6A1FzxepgTY http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RA6ybgDshSUfsdNR6NqNuwKHseUV-MP1Fd6A1FzxepgTY/assertion https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test http://purl.org/dc/terms/description A script (analysis.py in this directory) downloads the cluster file, selects representatives, queries the PDBe secondary_structure endpoint for each selected entry, extracts strand lengths for the representative chain, builds the histogram and computes (A)-(D). All raw per-chain strand lengths are written to strand_lengths.csv; the histogram to histogram.json. Every HTTP request carries the User-Agent 'delphisci-claim-test/1.0 (https://delphibio.org)' and no personal identifier. https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/Assessment https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: undefined undefined. Interpretation: https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of buehler-2008-hbond-confinement-04: supports, confidence 0.9 https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test http://www.w3.org/2000/01/rdf-schema#seeAlso https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/buehler-protein-materials/buehler-2008-hbond-confinement-04/result.json https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test http://www.w3.org/ns/prov#wasAttributedTo https://w3id.org/delphi/resource/agent/delphisci-claim-tester-inherit https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test https://w3id.org/delphi/ontology/admissibleDatasets Planned datasets: RCSB PDB 30%-sequence-identity cluster file (https://cdn.rcsb.org/resources/sequence/clusters/clusters-by-entity-30.txt); one representative polymer entity per cluster, the first listed, PDBe API secondary structure per entry (https://www.ebi.ac.uk/pdbe/api/pdb/entry/secondary_structure/{pdb_id}); strands per chain with start and end residue numbers, RCSB search API (https://search.rcsb.org/rcsbsearch/v2/query) or PDBe summary API to restrict to X-ray entries with resolution <= 2.5 A and polymer entity type protein https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test https://w3id.org/delphi/ontology/dataKind physical https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation Refutes if the mode is >= 8 residues or <= 2 residues, or if more than 30% of strands are longer than 10 residues. Any other failure of (A)-(D) -> mixed. If fewer than 2,000 representative chains with at least one strand can be retrieved, -> inconclusive. https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test https://w3id.org/delphi/ontology/evidenceAgainst All four pre-registered criteria pass on 60,263 strands from 5,000 representative chains, so the verdict is 'supports' for the distributional reading only; the causal reading was pre-registered as not testable here. The verdict depends on the pre-registered rule that excludes strand segments shorter than 2 residues: PDBe returns 17,577 one-residue strand segments among 77,840 raw segments (22.6%), and had they been kept the mode would be 1 residue, which the fail criterion labels 'refutes'. One-residue segments are most plausibly isolated beta-bridges rather than strands, which is why the exclusion was pre-registered, but a reader who regards them as strands should read the result as 'refutes'. Criterion (A) is passed narrowly: length 5 has 9,555 strands and length 4 has 9,404 (1.6% apart), with length 6 at 8,666 and lengths 2 and 3 at 8,327 and 8,016; the distribution is a broad plateau over 2 to 6 residues rather than a sharp peak, so the mode is in [3, 6] but would be fragile to a different assignment method. Strand assignments are PDBe's as served by the secondary_structure endpoint. The PDBe API documentation (openapi.json, retrieved 2026-11-08) describes them only as 'residue ranges of regular secondary structures (alpha helices and beta strands)' and does not name the method; whether they are the depositors' mmCIF struct_sheet_range records or a DSSP-style recomputation is not stated there and was not verified. Lengths use PDBe's mmCIF residue_number, so author numbering gaps do not affect them. Lengths are in residues, mapped to the model's 3-4 hydrogen bonds by the pre-registered assumption (band [3, 6] residues); no hydrogen bonds were measured. Sampling biases: the PDB over-represents crystallisable, well-folded proteins and the filter keeps only X-ray entries at or better than 2.5 A; the representative is the first entity of each cluster in file order (an arbitrary, not a quality-based, choice) and the first chain listed for that entity; clusters are at 30% sequence identity at the entity level, so fold-level redundancy remains; the 15,500 representatives screened are the first 5.7% of the 272,527 clusters, and the cluster file is sorted by cluster size, so the sample is drawn from the largest families; 631 chains with no strand of at least 2 residues were excluded by design, so the distribution is conditional on a chain having a strand; the exptl.method exact match on 'X-RAY DIFFRACTION' also admits hybrid X-ray entries. Eight filtered entries returned HTTP 404 from the secondary_structure endpoint and were skipped. https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test https://w3id.org/delphi/ontology/expectedObservation All of: (A) the mode of the strand-length histogram over the filtered set lies in [3, 6] residues; (B) the median strand length is <= 7 residues; (C) fewer than 15% of strands are longer than 10 residues; (D) the histogram is unimodal in the sense that counts decrease monotonically from the mode up to length 12 (ties allowed). -> supports (distributional reading only). https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test https://w3id.org/delphi/ontology/failCriterion Refutes if the mode is >= 8 residues or <= 2 residues, or if more than 30% of strands are longer than 10 residues. Any other failure of (A)-(D) -> mixed. If fewer than 2,000 representative chains with at least one strand can be retrieved, -> inconclusive. https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.9 https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-2 https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-3 https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test https://w3id.org/delphi/ontology/hasVerdict supports https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test https://w3id.org/delphi/ontology/hypothesis Across a non-redundant set of experimentally determined protein structures, the distribution of beta-strand lengths is concentrated at short strands, with its mode in the range that corresponds to the 3-4 hydrogen-bond cluster the Keten & Buehler (2008) model identifies as the shear-strength optimum, and long strands are rare. https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test https://w3id.org/delphi/ontology/inferenceMethod A script (analysis.py in this directory) downloads the cluster file, selects representatives, queries the PDBe secondary_structure endpoint for each selected entry, extracts strand lengths for the representative chain, builds the histogram and computes (A)-(D). All raw per-chain strand lengths are written to strand_lengths.csv; the histogram to histogram.json. Every HTTP request carries the User-Agent 'delphisci-claim-test/1.0 (https://delphibio.org)' and no personal identifier. https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test https://w3id.org/delphi/ontology/passCriterion All of: (A) the mode of the strand-length histogram over the filtered set lies in [3, 6] residues; (B) the median strand length is <= 7 residues; (C) fewer than 15% of strands are longer than 10 residues; (D) the histogram is unimodal in the sense that counts decrease monotonically from the mode up to length 12 (ties allowed). -> supports (distributional reading only). https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/buehler-2008-hbond-confinement-04 https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/buehler-2008-hbond-confinement-04--claim-test https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-1 http://purl.org/dc/terms/description https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-1 http://purl.org/dc/terms/license RCSB PDB data, free to use (https://www.rcsb.org/pages/usage-policy) https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-1 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/EvidenceItem https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-1 http://www.w3.org/2000/01/rdf-schema#label Dataset: RCSB PDB sequence clusters at 30% identity, entity level (one line per cluster, members as PDBID_ENTITY) https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://cdn.rcsb.org/resources/sequence/clusters/clusters-by-entity-30.txt https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-1 http://www.w3.org/ns/prov#wasDerivedFrom https://www.rcsb.org/docs/programmatic-access/file-download-services#sequence-clusters-data https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:60834fc4894a96f95e42efd647e26ce91adec7db1822d35ef2832c6f81711224 https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-2 http://purl.org/dc/terms/description https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-2 http://purl.org/dc/terms/license RCSB PDB data, free to use https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-2 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/EvidenceItem https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-2 http://www.w3.org/2000/01/rdf-schema#comment Location (not a URL): https://search.rcsb.org/rcsbsearch/v2/query (POST, 31 batches of up to 500 entity ids) https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-2 http://www.w3.org/2000/01/rdf-schema#label Dataset: RCSB Search API v2: entity ids in batch AND exptl.method = X-RAY DIFFRACTION AND rcsb_entry_info.resolution_combined <= 2.5 AND entity_poly.rcsb_entity_polymer_type = Protein; return_type polymer_entity https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-2 http://www.w3.org/ns/prov#wasDerivedFrom https://search.rcsb.org/ https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-3 http://purl.org/dc/terms/description https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-3 http://purl.org/dc/terms/license PDBe data, CC0 (https://www.ebi.ac.uk/pdbe/about/terms) https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-3 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/EvidenceItem https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-3 http://www.w3.org/2000/01/rdf-schema#comment Location (not a URL): https://www.ebi.ac.uk/pdbe/api/pdb/entry/secondary_structure/{pdb_id} (GET, one per filtered representative entry, gzip transfer) https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-3 http://www.w3.org/2000/01/rdf-schema#label Dataset: PDBe API secondary_structure per entry: helix and strand residue ranges per chain, mmCIF residue_number used https://w3id.org/delphi/resource/evidence/buehler-2008-hbond-confinement-04--claim-test--dataset-3 http://www.w3.org/ns/prov#wasDerivedFrom https://www.ebi.ac.uk/pdbe/api/doc/pdb.html https://w3id.org/np/RA6ybgDshSUfsdNR6NqNuwKHseUV-MP1Fd6A1FzxepgTY/provenance https://w3id.org/delphi/resource/agent/delphisci-claim-tester-inherit http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/ns/prov#SoftwareAgent https://w3id.org/delphi/resource/agent/delphisci-claim-tester-inherit http://www.w3.org/2000/01/rdf-schema#label delphisci claim tester (inherit; 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