@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 "The partitioning of MaSp1 and MaSp2 sequences into beta-sheet-forming poly-Ala tracts and 3_1-helix/beta-turn Gly-rich regions maps onto standard structural observables (DSSP classes and Ramachandran phi-psi angles). Although the authors' REMD coordinates were not deposited in the PDB, the sequences are public in UniProt, independent solid-state NMR and X-ray data exist, and REMD can be re-run in GROMACS. It is rated partially resolvable because re-running converged multi-chain REMD requires substantial compute and only the abstract is vendored locally."; dc:subject ; "Proposed test with existing data: Retrieve Nephila clavipes MaSp1 and MaSp2 repeat sequences from UniProt, perform replica-exchange MD (or inspect solid-state NMR chemical-shift constraints in BMRB), and compute residue-specific secondary structure via DSSP and backbone dihedral distributions on Ramachandran plots separately for poly-Ala segments and Gly-rich motifs. The claim is confirmed if poly-Ala tracts predominantly populate antiparallel beta-sheet states while GGX and GPGXX repeats populate 3_1-helical (polyglycine II-like) and beta-turn conformations."; "Gemini 4 Argon on buehler-2010-silk-assemblies-01: partially-resolvable, resolvability 0.72"; prov:wasAttributedTo ; "dataset-resolvability/0.2.0"; "Converging replica-exchange MD for multi-chain silk protein assemblies is computationally intensive and sensitive to force-field backbone dihedral potentials.", "The replica-exchange MD structural ensemble generated in the 2010 study is not deposited in the PDB or a public trajectory repository."; "0.85"^^xsd:double; , , ; "0.725"^^xsd:double; "partially-resolvable" . a ; dc:isPartOf ; dc:subject ; "Analysis feasibility of buehler-2010-silk-assemblies-01 by Gemini 4 Argon: 0.6"; prov:wasAttributedTo ; "dataset-resolvability/0.2.0/analysis-feasibility"; "0.6"^^xsd:double . a ; dc:isPartOf ; dc:subject ; "Data adequacy of buehler-2010-silk-assemblies-01 by Gemini 4 Argon: 0.65"; prov:wasAttributedTo ; "dataset-resolvability/0.2.0/data-adequacy"; "0.65"^^xsd:double . a ; dc:isPartOf ; dc:subject ; "Data existence of buehler-2010-silk-assemblies-01 by Gemini 4 Argon: 0.7"; prov:wasAttributedTo ; "dataset-resolvability/0.2.0/data-existence"; "0.7"^^xsd:double . a ; dc:isPartOf ; dc:subject ; "Discriminating power of buehler-2010-silk-assemblies-01 by Gemini 4 Argon: 0.8"; prov:wasAttributedTo ; "dataset-resolvability/0.2.0/discriminating-power"; "0.8"^^xsd:double . a ; dc:isPartOf ; dc:subject ; "Operationalizability of buehler-2010-silk-assemblies-01 by Gemini 4 Argon: 0.85"; prov:wasAttributedTo ; "dataset-resolvability/0.2.0/operationalizability"; "0.85"^^xsd:double . , , , , , . a ; dc:description "Public protein sequence records for Nephila clavipes spidroin-1 (MaSp1, P19837) and spidroin-2 (MaSp2, P46804)"; "Candidate dataset: UniProt Knowledgebase"; prov:wasDerivedFrom . a ; dc:description "Solid-state NMR chemical shifts and dihedral angle restraints for spider dragline silk poly-Ala and Gly-rich domains"; "Candidate dataset: Biological Magnetic Resonance Data Bank (BMRB)"; prov:wasDerivedFrom . a ; dc:description "Open-source MD engine supporting replica-exchange molecular dynamics and Ramachandran/DSSP structural analysis"; "Candidate dataset: GROMACS Molecular Dynamics Package"; 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-2010-silk-assemblies-01: partially-resolvable, resolvability 0.72"; . sub:sig npx:hasAlgorithm "RSA"; npx:hasPublicKey "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAyFHtPB6p0mCjDozxlOY9CmO3nBm7Te3jFbXyLmM+G1tGe47Da0jYIbhkl9Oo1ZjxmCa3LCwlEqK8gj6hEIcL4ahW30JXh9HycfKVk1bugkzMEV15tJdTzAU3sGMFnbNsn43xY2LFLy45tApkRm5byEiM7oRRrooIdwoQKnP4Wzq/bfAoJ9qvW+MGkelyOTd1jbSt+KfmT7xKmDfWzAHddUlWwMX2QJOLxDaffOteTop6ZRgPiNmPJKA/S62Gac9XtSYT3oDkZ6/nr5cxxNLpOyxTf5FPISiCe11xYO/unYjY+mwnOfA8yhJIyx1l0O9I0vpOpn+E5TvyHJV+oSTrvwIDAQAB"; npx:hasSignature "Xn8P0yXbj4Unday66wbIygA1DX9cR61om3iJzACoJhmkRQWhzomr+qOgUi2L34wk9GsaJ8PAuHxyL9uIHuJf7SOTAS3nOdh3v/XGg7ZhGuoUELuqODyF6Bw9MG/GsXc4TGMVrQx7a56dGgvdD0RFG94MDGkJ0YvqqmX4Jy4bRTSWST/siFkEh4KtmiVk2Z3LboxoqWMPD9coVhNuzsxHbZQ/48F7Kkb9DVRptsknaHrYQA0a/bS8GE1jZzD9+ZCs3x1x8oxvLCb6r6UEeY2dwffhJlN+/r7t+VnumcV7w3ePePXkbFQpbN+F0em3AqCUyWgntKsCFCf9LE9n0L0t+g=="; npx:hasSignatureTarget this:; npx:signedBy . }