{"paper":{"title":"Orientation-Dependent Protein Binding at Nanoparticle Interfaces","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"Docking and united-atom models match protein orientations at nanoparticle surfaces","cross_cats":["physics.comp-ph"],"primary_cat":"physics.bio-ph","authors_text":"Ian Rouse, Nicolae-Viorel Buchete, Vigneshwari Karunakaran Annapoorani, Vladimir Lobaskin","submitted_at":"2026-04-28T19:52:51Z","abstract_excerpt":"Accurate quantification of protein-nanoparticle interactions is essential for applications in nanobiotechnology, nanomedicine, and drug delivery. Motivated by recent computational and experimental work, we combine coarse-grained united-atom (UA) models with molecular docking to characterize protein adsorption on SiO_2 nanoparticles. We construct orientation-resolved heatmaps in which polar and azimuthal angles uniquely specify the relative protein-nanoparticle pose, and the map amplitude reports binding propensity via the minimum UA adsorption energy or the docking score. Each angular bin corr"},"claims":{"count":4,"items":[{"kind":"strongest_claim","text":"We find encouraging agreement between the two approaches in several cases, while also identifying limitations and routes for improvement, including optimized angular resolution and iterative refinement of interaction parameters.","source":"verdict.strongest_claim","status":"machine_extracted","claim_id":"C1","attestation":"unclaimed"},{"kind":"weakest_assumption","text":"That the minimum UA adsorption energy or docking score in each angular bin accurately reports binding propensity and that Jensen-Shannon divergence between the resulting orientational distributions reliably indicates that docking score landscapes relate to Boltzmann-averaged UA adsorption energetics.","source":"verdict.weakest_assumption","status":"machine_extracted","claim_id":"C2","attestation":"unclaimed"},{"kind":"one_line_summary","text":"A computational framework creates orientation heatmaps of protein adsorption on SiO2 nanoparticles by combining united-atom models and docking, then compares results for eight allergen proteins using Jensen-Shannon divergence to assess agreement between the methods.","source":"verdict.one_line_summary","status":"machine_extracted","claim_id":"C3","attestation":"unclaimed"},{"kind":"headline","text":"Docking and united-atom models match protein orientations at nanoparticle surfaces","source":"verdict.pith_extraction.headline","status":"machine_extracted","claim_id":"C4","attestation":"unclaimed"}],"snapshot_sha256":"4f9d86c97bacee19a1164fbda8ab853c17d547ba5b6fae7bd847199441b9d05e"},"source":{"id":"2604.26086","kind":"arxiv","version":2},"verdict":{"id":"4cf8f105-e04d-4c22-9a06-ac0748d449e8","model_set":{"reader":"grok-4.3"},"created_at":"2026-05-19T17:47:25.912696Z","strongest_claim":"We find encouraging agreement between the two approaches in several cases, while also identifying limitations and routes for improvement, including optimized angular resolution and iterative refinement of interaction parameters.","one_line_summary":"A computational framework creates orientation heatmaps of protein adsorption on SiO2 nanoparticles by combining united-atom models and docking, then compares results for eight allergen proteins using Jensen-Shannon divergence to assess agreement between the methods.","pipeline_version":"pith-pipeline@v0.9.0","weakest_assumption":"That the minimum UA adsorption energy or docking score in each angular bin accurately reports binding propensity and that Jensen-Shannon divergence between the resulting orientational distributions reliably indicates that docking score landscapes relate to Boltzmann-averaged UA adsorption energetics.","pith_extraction_headline":"Docking and united-atom models match protein orientations at nanoparticle surfaces"},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2604.26086/integrity.json","findings":[],"available":true,"detectors_run":[{"name":"doi_compliance","ran_at":"2026-05-19T20:33:26.690123Z","status":"completed","version":"1.0.0","findings_count":0}],"snapshot_sha256":"95214e680eb38d59ab18ae9b93d5623babfada69a2cb2b7a11d1c2de6ed062db"},"references":{"count":50,"sample":[{"doi":"","year":2008,"title":"I. Lynch and K. Dawson, “Protein- nanoparticle interactions,”Nano Today, vol. 3, pp. 40–47, 2008","work_id":"75b82439-06cc-42e9-92f9-2ad2782e6479","ref_index":1,"cited_arxiv_id":"","is_internal_anchor":false},{"doi":"","year":2016,"title":"Kinet- ics of the formation of a protein corona around nanoparticles,","work_id":"88000326-1adc-4010-b121-df932cf21295","ref_index":2,"cited_arxiv_id":"","is_internal_anchor":false},{"doi":"","year":2024,"title":"Un- derstanding protein-nanoparticle inter- actions leading to protein corona for- mation: In vitro - in vivo correlation study,","work_id":"5e4818f7-7862-4c49-a044-9c84ac669a85","ref_index":3,"cited_arxiv_id":"","is_internal_anchor":false},{"doi":"","year":2023,"title":"A computational view on nanomaterial intrinsic and ex- trinsic features for nanosafety and sus- tainability,","work_id":"7a373b79-f2b2-4005-9171-3dbc50b5f7ef","ref_index":4,"cited_arxiv_id":"","is_internal_anchor":false},{"doi":"","year":2050,"title":"Un- derstanding the nanoparticle–protein corona using methods to quantify ex- change rates and affinities of proteins for nanoparticles,","work_id":"4362e36a-f957-4e9c-ad9a-8948cf75c1a2","ref_index":5,"cited_arxiv_id":"","is_internal_anchor":false}],"resolved_work":50,"snapshot_sha256":"faafb208b75105acb08dde6048b546ceebc9d28c84ae8bd34a0f96416d1a72ca","internal_anchors":0},"formal_canon":{"evidence_count":1,"snapshot_sha256":"edec05283a0a0fde2001bddd1c834dbca91ec1e922551d47f7f183f14638826b"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}