ORIGINAL RESEARCH article
Front. Chem.
Sec. Theoretical and Computational Chemistry
Entangled Fingerprints for Quantum-encoded Chemoinformatics: Quantum Circuits for Molecular Similarity in the Noisy Era
Provisionally accepted
- 1ITMO University, Saint Petersburg, Russia
- 2Julius-Maximilians-Universitat Wurzburg, Würzburg, Germany
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Quantum computing holds promise for molecular similarity analysis in chemoinformatics and drug discovery. We propose a quantum circuit to encode the classically pre-computed Tanimoto similarity (T), obtained from extended-connectivity fingerprints (ECFPs) with RDKit, into a compact three-qubit entangled state using Qiskit. A 3-qubit circuit with RY rotations encodes T coefficients, while CNOT gates create an entangled three-qubit state that serves as a sensitive probe for quantum noise and error-mitigation performance. Simulations under noise demonstrate that exponential mitigation reduces errors by 75.0% for similar pairs (e.g., aspirin–aspirin) and 87.5% for dissimilar pairs (e.g., aspirin–butane) at a 1% error rate, maintaining fidelity within ±0.001 deviation. At 10% depolarization noise, error reduction drops to 25.0% and 17.4% for these pairs, respectively. The overall results show that the , mitigation is proportionally more effective for low-similarity pairs. Experiments on IBM Quantum hardware confirm Z-basis reliability but reveal challenges with X-basis noise. Our work demonstrates quantum-encoded T representation and recovery on NISQ devices as a proof-of-concept, highlighting the critical role of error mitigation in hybrid quantum-classical workflows.
Keywords: Extended-connectivity fingerprints, Near-term Quantum Computing, noise mitigation, Quantum-encoded chemoinformatics, Tanimoto similarity
Received: 17 Sep 2025; Accepted: 10 Dec 2025.
Copyright: © 2025 Shityakov and Dandekar. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Sergey Shityakov
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