{"paper":{"title":"Reduced-Alphabet QUBO/Ising Formulation for Constraint-Driven Cyclic Peptide Sequence Design","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["q-bio.BM"],"primary_cat":"physics.chem-ph","authors_text":"Xin Li, Yan Zhou, Yuqi Wang","submitted_at":"2026-06-22T12:34:39Z","abstract_excerpt":"Cyclic peptide design requires balancing local residue preferences with constraints from ring-forming chemistry, residue spacing, topology, target compatibility, and developability. Here, we present a reduced-alphabet quadratic unconstrained binary optimization (QUBO)/Ising formulation for constraint-driven cyclic peptide sequence design. Amino acids are grouped into physicochemical or interaction-based residue classes, and peptide positions are represented by binary residue-class assignment variables. The objective combines one-hot sequence validity, cyclization constraints, optional target-c"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2606.23253","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2606.23253/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}