This record contains the QSCE-Allostery BCR-ABL1 Benchmark Note, documenting a second-target topology-only quantum allostery validation study performed under Marrakesh-derived backend noise.
The benchmark evaluates whether the QSCE-Allostery workflow, previously strengthened on KRAS G12C, can generalize to BCR-ABL1, a structurally distinct tyrosine kinase allostery target. The workflow uses static apo structure input, avoids classical molecular dynamics trajectory input, constructs a coarse-grained residue contact topology, executes a compact 12-qubit quantum graph-propagation kernel under backend-derived noise, and ranks candidate allosteric regions by active-site-coupled quantum connectivity response.
For this BCR-ABL1 benchmark, the apo input structure was 1OPL filtered to chain A, and the holo validation structure was 5MO4 filtered to chain A. The validation ligand was restricted to AY7602A, corresponding to the AY7 allosteric/myristoyl-pocket ligand environment, while NIL601A was excluded from final validation scoring to avoid contaminating the allosteric-pocket evaluation with catalytic-site or non-target holo contacts.
Across three independent Marrakesh-noise simulator seeds, QSCE-Allostery produced a stable AY7-only top-5 hit rate of 2/5 = 0.400. In all three runs, the same two candidate regions, PRO458A..CYS494A and PRO421A..SER457A, overlapped the AY7 myristoyl/allosteric validation pocket. Together, these regions captured 13 of 23 AY7-only validation contact residues, corresponding to 56.5% residue-level recovery of the AY7 contact set within the QSCE top-5 regions.
The record also documents comparison against simple classical graph baselines. Across all three BCR-ABL1 seeds, QSCE matched the strongest simple active-site-proximity baselines, shortest-path-to-active and diffusion-to-active, while exceeding weighted degree, betweenness, and PageRank. A PyMOL-based visualization package was generated to project active-site anchors, QSCE top-5 candidate regions, AY7 validation contacts, and QSCE/AY7 overlap residues onto apo BCR-ABL1 chain A.
This benchmark is presented as a strengthened second-target prototype result. It does not claim universal allosteric prediction capability or clinical validation. Rather, it provides early evidence that QSCE-Allostery is beginning to generalize beyond KRAS G12C by recovering repeatable ligand-relevant allosteric enrichment in a second, structurally distinct protein target using the same topology-only quantum workflow.
Key result summary:
• Target: BCR-ABL1
• Apo input: 1OPL chain A
• Holo validation: 5MO4 chain A
• Validation ligand: AY7602A / AY7
• Excluded ligand from final scoring: NIL601A
• Coarse-grained nodes: 12
• Quantum register size: 12 qubits
• Noise model: IBM Marrakesh-derived Aer backend noise
• Representative baseline transpiled depth: 897, with additional diagnostic/control circuits reaching depths of 866--1035
• Shots per scan: 1024
• Simulator seeds: 101, 202, 303
• Top-5 AY7-only hit rate: 2/5 = 0.400 across all three seeds
• AY7 contact residues recovered inside QSCE top-5 regions: 13/23 = 0.565
• Recurrent QSCE hit regions: PRO458A..CYS494A and PRO421A..SER457A
• Classical baseline result: QSCE matched shortest-path-to-active and diffusion-to-active while exceeding weighted degree, betweenness, and PageRank
• Visualization: PyMOL structural projection of QSCE top-5 regions, AY7 contacts, and QSCE/AY7 overlap residues
This record is part of the QSCE-Allostery benchmark series for the Cleveland Clinic Global Quantum + AI Challenge and supports the broader evaluation of QSCE-derived topology-only quantum signal propagation for upstream allosteric site prioritization.
