Cleveland Clinic, RIKEN, and IBM Model a 12,635-Atom Protein - the Largest Known to Be Simulated with Quantum Computers

Milestone simulation of biologically meaningful molecules expands quantum-centric supercomputing's role as a scientific tool

YORKTOWN HEIGHTS, N.Y. and CLEVELAND, May 5, 2026 /PRNewswire/ -- Scientists at Cleveland Clinic, RIKEN, and IBM (NYSE: IBM) have used IBM quantum computers and two of the world's most powerful supercomputers to simulate protein complexes spanning up to 12,635 atoms. These are the largest-known simulations of biologically meaningful molecules performed with quantum hardware yet, and signal that quantum computers are maturing into useful scientific tools which can help solve fundamental problems in biology, chemistry, and life sciences.

The results were achieved in part by an innovative algorithm that optimizes how quantum and classical computers can work together, a framework known as quantum-centric supercomputing. Using this approach, the team captured the behavior of two biochemically relevant proteins that are roughly 40 times larger than what this same method could initially achieve just six months ago. Additionally, the accuracy of the simulations in a key step of the workflow improved by up to 210 times over this same period.

The decision to explore if quantum computers could offer value in the simulation of protein complexes was motivated by challenges faced today by researchers when studying how a drug candidate could bind to a protein. This can be one of the most difficult and expensive problems in life sciences research, and one that today's existing computational methods have struggled to exactly solve as molecules increase in size. Doing so accurately and early in the discovery process could meaningfully shorten drug development timelines that currently can stretch over a decade and require substantial investment to produce a single medicine.

"This work marks an important advance and underscores quantum computing's emerging role on systems of relevance to drug discovery," said Kenneth Merz, Ph.D., lead author of the study and staff scientist in Cleveland Clinic's Computational Life Sciences Department. "By crossing the 12,000-atom barrier, we have significantly expanded the scale of biologically meaningful molecular simulations possible with quantum computing and demonstrated a framework for applying these methods to scientifically relevant problems at a larger scale."

"For years, quantum computing has been a promise. Now, quantum computers are producing results that matter to science," said Jay Gambetta, Director of IBM Research and IBM Fellow. "The systems we simulated here are the kind of molecules that biologists and chemists work with in the real world. Quantum computers are no longer proving they are viable tools – they are proving they can contribute meaningful results in quantum-centric supercomputing architectures."

The breakthrough research, reported in a pre-print study, builds on a series of milestones from the three institutions. This includes work on the cover of Science Advances that introduced techniques to model electronic states in molecules, first demonstrated on iron sulfides, and more recently, the 303-atom benchmark molecule called Trp-cage – the first-known full quantum-centric simulation made of 20 amino acids.

Quantum and Classical Computers, Working in Tandem

This approach – what IBM calls quantum-centric supercomputing – pairs quantum processors with classical computers so each computational tool can solve the parts of a problem where it excels. In this work, classical computers deconstructed the protein-ligand complexes into computable fragments. IBM's 156-qubit IBM Quantum Heron processors, running within the IBM quantum computers at both Cleveland Clinic in the United States and RIKEN in Japan, calculated the quantum-mechanical behavior of those pieces in tandem with two of the most powerful classical supercomputers – Fugaku at RIKEN and Miyabi-G, operated by the University of Tokyo and the University of Tsukuba. The strength of IBM's quantum hardware was essential to the accuracy and success of the computation, which required up to 94 qubits running nearly 6,000 quantum operations within certain parts of the simulation. Results were reassembled on classical computers to obtain a complete representation of the molecule.

As published on arXiv, the jump in scale was made possible by both algorithmic innovation and access to cutting-edge computing infrastructure. The novel quantum-classical hybrid algorithm, coined EWF-TrimSQD, dramatically reduced computational overhead and accelerated the ability to directly represent the chemistry of these molecular systems on quantum hardware. As a result, the frontier for what is possible with quantum-centric supercomputing has been pushed forward to previously inaccessible molecule sizes, and there is a clear path to further increase the size and accuracy of such calculations.

A Step Towards Drug Discovery

The team views this work as a starting point. Looking ahead, the ability to scale simulations of molecular systems with accuracy is a step towards helping researchers better predict how medicines may interact with protein targets. Computational improvements in drug discovery rest on two fundamental capabilities: first, modeling the movement of atoms as biological processes unfold; and second, accurately computing their energies, for which these results provide evidence that quantum‑centric supercomputing can support.

As quantum computers advance, integrating them into computational workflows could offer higher accuracy in energy calculations at larger scales, and potentially open the door to simulating enzyme catalysts, drug mechanisms, and other molecular behaviors that today can only be studied through experimentation.

More broadly, this breakthrough marks a shift in what quantum computing means to science. For most of its history, the field of quantum computation has measured progress in qubits, gates, and error rates. Now, its capabilities can also be measured by the size and significance of the problems it can help to solve.

For more information on this milestone, visit: https://www.ibm.com/quantum/blog/cleveland-clinic-riken-chemistry

Research Support

This research is supported by NEDO (New Energy and Industrial Technology Development Organization), an organization under the jurisdiction of Japan's Ministry of Economy, Trade and Industry (METI)'s "Research and Development of Quantum-Supercomputers Hybrid Platform for Exploration of Uncharted Computable Capabilities" (Project Leader: Mitsuhisa Sato) as part of the "Project for Research and Development of Enhanced Infrastructures for Post 5G Information and Communications Systems (JPNP20017)."

About IBM

IBM is a leading global hybrid cloud and AI, and business services provider, helping clients in more than 175 countries capitalize on insights from their data, streamline business processes, reduce costs and gain the competitive edge in their industries. Thousands of governments and corporate entities in critical infrastructure areas such as financial services, telecommunications and healthcare rely on IBM's hybrid cloud platform and Red Hat OpenShift to affect their digital transformations quickly, efficiently and securely. IBM's breakthrough innovations in AI, quantum computing, industry-specific cloud solutions and business services deliver open and flexible options to our clients. All of this is backed by IBM's legendary commitment to trust, transparency, responsibility, inclusivity and service.
For more information, visit https://research.ibm.com.

About Cleveland Clinic

Cleveland Clinic is a nonprofit multispecialty academic medical center that integrates clinical and hospital care with research and education. Founded in 1921 by four renowned physicians with a vision of providing outstanding patient care based upon the principles of cooperation, compassion and innovation, Cleveland Clinic has pioneered many medical breakthroughs, including coronary artery bypass surgery and the first face transplant in the United States. Cleveland Clinic is consistently recognized in the U.S. and throughout the world for its expertise and care. Among Cleveland Clinic's 83,000 employees worldwide are more than 6,600 salaried physicians and researchers, and 21,900 registered nurses and advanced practice providers, representing 140 medical specialties and subspecialties. Cleveland Clinic is a 6,725-bed health system that includes a 173-acre main campus near downtown Cleveland, 23 hospitals, 300 outpatient facilities, including locations in northeast Ohio; Florida; Las Vegas, Nevada; Toronto, Canada; Abu Dhabi, UAE; and London, England. In 2025, there were 15.9 million outpatient encounters, 343,000 hospital admissions and observations, and 336,000 surgeries and procedures throughout Cleveland Clinic's health system. Visit us at clevelandclinic.org. Follow us at x.com/CleClinicNews. News and resources are available at newsroom.clevelandclinic.org.

Media contacts

Brittany Forgione
IBM
Brittany.Forgione@ibm.com

Erin Angelini
IBM Research Communications
edlehr@us.ibm.com

Alicia Reale-Cooney
Cleveland Clinic
realeca@ccf.org  
216.408.7444

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