Nanopublication

< Home

ID

https://w3id.org/np/RA8n_YmgpJFj_eALtWkCcMZjxJ3s66vbtVFTGwgwGu7Wg

Formats

.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt

Content

@prefix this: <https://w3id.org/np/RA8n_YmgpJFj_eALtWkCcMZjxJ3s66vbtVFTGwgwGu7Wg> .
@prefix sub: <https://w3id.org/np/RA8n_YmgpJFj_eALtWkCcMZjxJ3s66vbtVFTGwgwGu7Wg/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix dc: <http://purl.org/dc/terms/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

sub:Head {
  this: a np:Nanopublication;
    np:hasAssertion sub:assertion;
    np:hasProvenance sub:provenance;
    np:hasPublicationInfo sub:pubinfo .
}

sub:assertion {
  <https://w3id.org/delphi/resource/claim/buehler-2010-helix-sheet-01> a <https://w3id.org/delphi/ontology/Claim>;
    dc:description "In coiled-coil proteins under tension the alpha-to-beta transition is controlled by alpha-helix length: in the asymptotic limit, helices shorter than 26 amino acids or 3.8 nm slide past each other, whereas longer ones undergo the alpha-to-beta transition.";
    dc:type "mathematical-law";
    <http://www.w3.org/2000/01/rdf-schema#comment> "Notation basis: Threshold stated in the abstract; the derivation (balance of sliding versus unfolding energy) is in the full text.";
    <http://www.w3.org/2000/01/rdf-schema#label> "Alpha-helices shorter than 26 residues (3.8 nm) slide; longer ones convert to beta-sheet under stretch";
    <http://www.w3.org/2004/02/skos/core#notation> "L^{*} = 26\\ \\text{residues} \\approx 3.8\\ \\mathrm{nm}:\\quad L < L^{*} \\Rightarrow \\text{sliding},\\ L > L^{*} \\Rightarrow \\alpha\\to\\beta";
    <https://w3id.org/delphi/ontology/context> "Zhao Qin et al., “Molecular Dynamics Simulation of theα-Helix toβ-Sheet Transition in Coiled Protein Filaments: Evidence for a Critical Filament Length Scale”, Physical Review Letters 104 (2010), doi:10.1103/physrevlett.104.198304; Abstract. Scope: Alpha-helical coiled-coil proteins of varying length under stretch (MD and theory)" .
}

sub:provenance {
  <https://doi.org/10.1103/physrevlett.104.198304> a <https://schema.org/CreativeWork>;
    dc:bibliographicCitation "Zhao Qin, Markus J. Buehler. Molecular Dynamics Simulation of theα-Helix toβ-Sheet Transition in Coiled Protein Filaments: Evidence for a Critical Filament Length Scale. Physical Review Letters 104 (2010). doi:10.1103/physrevlett.104.198304";
    dc:creator "Zhao Qin, Markus J. Buehler";
    dc:date "2010"^^xsd:gYear;
    dc:identifier "doi:10.1103/physrevlett.104.198304", "pmid:20867006";
    dc:title "Molecular Dynamics Simulation of theα-Helix toβ-Sheet Transition in Coiled Protein Filaments: Evidence for a Critical Filament Length Scale" .
  
  <https://w3id.org/delphi/resource/agent/delphisci-buehler-protein-materials-extractor>
    a prov:SoftwareAgent;
    <http://www.w3.org/2000/01/rdf-schema#label> "delphisci buehler-protein-materials claim extractor";
    prov:actedOnBehalfOf <https://orcid.org/0009-0007-4948-9192>;
    <https://w3id.org/delphi/ontology/usesModel> <https://w3id.org/delphi/resource/model/claude-fable-5.1> .
  
  <https://w3id.org/delphi/resource/model/claude-fable-5.1> a <https://w3id.org/delphi/ontology/LanguageModel>;
    <http://www.w3.org/2000/01/rdf-schema#label> "Claude Fable 5.1" .
  
  sub:assertion prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-buehler-protein-materials-extractor>;
    prov:wasDerivedFrom <https://doi.org/10.1103/physrevlett.104.198304>, sub:quote;
    prov:wasGeneratedBy sub:extraction .
  
  sub:extraction a prov:Activity;
    prov:qualifiedAssociation sub:extractionPlan;
    prov:used <https://github.com/fractastical/delphisci/blob/b89a0890bee05ef18f8202387085854fac3ca776/claim-sources/buehler-protein-materials/inputs/sources.json>,
      <https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI:10.1103/physrevlett.104.198304&resultType=core&format=json>;
    prov:wasAssociatedWith <https://w3id.org/delphi/resource/agent/delphisci-buehler-protein-materials-extractor> .
  
  sub:extractionPlan prov:hadPlan <https://github.com/fractastical/delphisci/blob/b89a0890bee05ef18f8202387085854fac3ca776/claim-sources/buehler-protein-materials/build/generate.mjs> .
  
  sub:quote a prov:Entity;
    <http://www.w3.org/2000/01/rdf-schema#comment> "Quoted from the published abstract as returned by Europe PMC (2010-helix-sheet.abstract.txt, sha256 ff3d9af312f17efad8cd63a0b625adaecca946740d011c905ff3e86d566bf132); the full text was not read (not in Europe PMC open-access subset). Checked by build/check.py.";
    prov:hadPrimarySource <https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI:10.1103/physrevlett.104.198304&resultType=core&format=json>;
    prov:wasQuotedFrom <https://doi.org/10.1103/physrevlett.104.198304>;
    <https://schema.org/text> "In the asymptotic limit, short proteins with less than 26 amino acids or 3.8 nm length reveal interprotein sliding, whereas proteins with greater lengths feature an α-β transition, leading to a significant increase in the protein's stiffness, strength, and energy dissipation capacity at large deformation." .
  
  sub:sourceChecksum <http://spdx.org/rdf/terms#algorithm> <http://spdx.org/rdf/terms#checksumAlgorithm_sha256>;
    <http://spdx.org/rdf/terms#checksumValue> "ff3d9af312f17efad8cd63a0b625adaecca946740d011c905ff3e86d566bf132";
    <http://www.w3.org/2000/01/rdf-schema#comment> "Checksum of the vendored text file inputs/2010-helix-sheet.abstract.txt, not of the publisher's copy." .
  
  <https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI:10.1103/physrevlett.104.198304&resultType=core&format=json>
    a prov:Entity;
    <http://spdx.org/rdf/terms#checksum> sub:sourceChecksum;
    <http://www.w3.org/2000/01/rdf-schema#label> "Abstract of Molecular Dynamics Simulation of theα-Helix toβ-Sheet Transition in Coiled Protein Filaments: Evidence for a Critical Filament Length Scale, as read";
    <https://schema.org/about> <https://doi.org/10.1103/physrevlett.104.198304> .
}

sub:pubinfo {
  <https://w3id.org/delphi/resource/domain/buehler-protein-materials> <http://www.w3.org/2000/01/rdf-schema#label>
      "buehler-protein-materials" .
  
  this: dc:created "2026-11-08T04:38:11.893Z"^^xsd:dateTime;
    dc:creator <https://orcid.org/0009-0007-4948-9192>;
    dc:license <https://creativecommons.org/licenses/by/4.0/>;
    npx:hasNanopubType <https://w3id.org/delphi/ontology/Claim>;
    npx:introduces <https://w3id.org/delphi/resource/claim/buehler-2010-helix-sheet-01>;
    <http://www.w3.org/2000/01/rdf-schema#label> "Zhao Qin et al. 2010 claim: Alpha-helices shorter than 26 residues (3.8 nm) slide; longer ones convert to beta-sheet under stretch";
    <https://w3id.org/delphi/ontology/domain> <https://w3id.org/delphi/resource/domain/buehler-protein-materials> .
  
  sub:sig npx:hasAlgorithm "RSA";
    npx:hasPublicKey "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAyFHtPB6p0mCjDozxlOY9CmO3nBm7Te3jFbXyLmM+G1tGe47Da0jYIbhkl9Oo1ZjxmCa3LCwlEqK8gj6hEIcL4ahW30JXh9HycfKVk1bugkzMEV15tJdTzAU3sGMFnbNsn43xY2LFLy45tApkRm5byEiM7oRRrooIdwoQKnP4Wzq/bfAoJ9qvW+MGkelyOTd1jbSt+KfmT7xKmDfWzAHddUlWwMX2QJOLxDaffOteTop6ZRgPiNmPJKA/S62Gac9XtSYT3oDkZ6/nr5cxxNLpOyxTf5FPISiCe11xYO/unYjY+mwnOfA8yhJIyx1l0O9I0vpOpn+E5TvyHJV+oSTrvwIDAQAB";
    npx:hasSignature "k/Y0ifHD5rGY2qEtJAL9xgrJjtwaTyJAgiek1tlGx78qo3ibW1xECTXR5+Pkvr6oMB3tGICCgLH38hwldXLV0T8QKPmWyzhopRe72+23YA/SyYDr1wurh37BPlK5mbLCPHgeaxOOWELpy6BjF756rnTZ6xQMU95tqLfLSeWcMFu4yw/ZsyeosYslq3UUZU3UmEhUVk5v/sB7Lr8NO+dNqhs1FiGdDNmBeapfir0E8azCWdu2P8QGw25oS+QTKVUxsP7N04QUnmZcbrID01oAnScQ3ozoH0RvBDtWYmm2tqCExhLRVcVjBJnxrG0KGEPWWnpQvDASjwe+EPbitHbI4A==";
    npx:hasSignatureTarget this:;
    npx:signedBy <https://orcid.org/0009-0007-4948-9192> .
}