@prefix this: . @prefix sub: . @prefix np: . @prefix rdf: . @prefix prov: . @prefix npx: . @prefix dc: . @prefix xsd: . sub:Head { this: a np:Nanopublication; np:hasAssertion sub:assertion; np:hasProvenance sub:provenance; np:hasPublicationInfo sub:pubinfo . } sub:assertion { a prov:SoftwareAgent; "delphisci dataset-resolvability assessor (Gemini 4 Argon)"; prov:actedOnBehalfOf ; . a ; dc:description "Human type I collagen sequences and triple-helical structural templates are openly available in UniProt and the PDB, and open MD codes with standard CHARMM parameters can test whether motif substitutions significantly alter triple-helix stiffness. However, because the original simulation scripts are not archived and the abstract omits the exact motif identities and pulling protocol, independent verification requires reconstructing the setup or comparing against indirect structural flexibility proxies in PDB crystal structures."; dc:subject ; "Proposed test with existing data: Construct atomistic triple-helical tropocollagen segments for distinct Gly-X-Y sequence motifs from human type I collagen using PDB triple-helix templates and UniProt sequences, run steered molecular dynamics tensile pulls in GROMACS or NAMD with CHARMM force fields, and test whether the tangent Young's modulus varies significantly across motifs."; "Gemini 4 Argon on buehler-2009-tropocollagen-sequencing-01: partially-resolvable, resolvability 0.67"; prov:wasAttributedTo ; "dataset-resolvability/0.2.0"; "Direct single-molecule experimental stiffness measurements resolved at the level of individual Gly-X-Y motifs do not exist in public repositories, making the test reliant on MD re-implementation.", "The abstract alone does not specify which four exact Gly-X-Y motifs, pulling velocities, or boundary conditions were used in the original simulations."; "0.78"^^xsd:double; , , ; "0.673"^^xsd:double; "partially-resolvable" . a ; dc:isPartOf ; dc:subject ; "Analysis feasibility of buehler-2009-tropocollagen-sequencing-01 by Gemini 4 Argon: 0.72"; prov:wasAttributedTo ; "dataset-resolvability/0.2.0/analysis-feasibility"; "0.72"^^xsd:double . a ; dc:isPartOf ; dc:subject ; "Data adequacy of buehler-2009-tropocollagen-sequencing-01 by Gemini 4 Argon: 0.55"; prov:wasAttributedTo ; "dataset-resolvability/0.2.0/data-adequacy"; "0.55"^^xsd:double . a ; dc:isPartOf ; dc:subject ; "Data existence of buehler-2009-tropocollagen-sequencing-01 by Gemini 4 Argon: 0.65"; prov:wasAttributedTo ; "dataset-resolvability/0.2.0/data-existence"; "0.65"^^xsd:double . a ; dc:isPartOf ; dc:subject ; "Discriminating power of buehler-2009-tropocollagen-sequencing-01 by Gemini 4 Argon: 0.68"; prov:wasAttributedTo ; "dataset-resolvability/0.2.0/discriminating-power"; "0.68"^^xsd:double . a ; dc:isPartOf ; dc:subject ; "Operationalizability of buehler-2009-tropocollagen-sequencing-01 by Gemini 4 Argon: 0.78"; prov:wasAttributedTo ; "dataset-resolvability/0.2.0/operationalizability"; "0.78"^^xsd:double . , , , , , . a ; dc:description "Collagen-like triple-helical peptide crystal and NMR structures used as structural templates and for sequence-dependent helical pitch and B-factor comparisons"; "Candidate dataset: RCSB Protein Data Bank"; prov:wasDerivedFrom . a ; dc:description "Canonical human type I collagen alpha-1 (P02452) and alpha-2 (P08123) sequences from which physiological Gly-X-Y motifs are selected"; "Candidate dataset: UniProt Knowledgebase"; prov:wasDerivedFrom . a ; dc:description "Open-source molecular dynamics package capable of re-running steered MD tensile tests on tropocollagen triple-helix segments"; "Candidate dataset: GROMACS"; prov:wasDerivedFrom . a ; dc:identifier "gemini-4-argon-medium"; "Gemini 4 Argon" . } sub:provenance { sub:assertion prov:wasAttributedTo ; prov:wasDerivedFrom , ; prov:wasGeneratedBy sub:assessment . sub:assessment a prov:Activity; prov:qualifiedAssociation sub:assessmentPlan; prov:wasAssociatedWith . sub:assessmentPlan prov:hadPlan . } sub:pubinfo { "buehler-protein-materials" . this: dc:created "2026-11-08T04:48:50.317Z"^^xsd:dateTime; dc:creator ; dc:license ; npx:hasNanopubType ; npx:introduces ; "Gemini 4 Argon on buehler-2009-tropocollagen-sequencing-01: partially-resolvable, resolvability 0.67"; . sub:sig npx:hasAlgorithm "RSA"; npx:hasPublicKey "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAyFHtPB6p0mCjDozxlOY9CmO3nBm7Te3jFbXyLmM+G1tGe47Da0jYIbhkl9Oo1ZjxmCa3LCwlEqK8gj6hEIcL4ahW30JXh9HycfKVk1bugkzMEV15tJdTzAU3sGMFnbNsn43xY2LFLy45tApkRm5byEiM7oRRrooIdwoQKnP4Wzq/bfAoJ9qvW+MGkelyOTd1jbSt+KfmT7xKmDfWzAHddUlWwMX2QJOLxDaffOteTop6ZRgPiNmPJKA/S62Gac9XtSYT3oDkZ6/nr5cxxNLpOyxTf5FPISiCe11xYO/unYjY+mwnOfA8yhJIyx1l0O9I0vpOpn+E5TvyHJV+oSTrvwIDAQAB"; npx:hasSignature "m+TA99TYFxEMS7GpGmrSuCnbqBpWtqAalejeYqvBOs5mheeuR/TBWiCwN2fSTKoLImJNLBye9LCaELqUqC/LtqHScBmbO9RuMgTznr4ngWYV5+7mMlPsCb+k3X99XwQ3449saeblqdulMo7sM9r9f6oy+qzu6MogmpehDwHcr3gEfI4XhTbzyG+4fWKCBhkoXz3r7ZC2CNl0fWDkP+anRIUXIfnokwpMeKTyu5DJrr3TwDunx9y6Irb3IyzKIPc+6tLdN5RT6FxyGuoAhmIC6bGP45mIY1AbuHXfF6Gd29tT/+tlR0mHM7c+PFpHcSSKn3vqO3NeD9rqk9t6AhjKbg=="; npx:hasSignatureTarget this:; npx:signedBy . }