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Related Concept Videos

Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
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Protein Dynamics in Living Cells

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Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

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Molecular Models02:00

Molecular Models

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Proteomics01:33

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Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
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Updated: Jun 6, 2026

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
07:33

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

Molecular Quantum Computations on a Protein.

Akhil Shajan1, Danil Kaliakin1, Fangchun Liang1

  • 1Center for Computational Life Sciences, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44106, United States.

Journal of Chemical Theory and Computation
|June 4, 2026
PubMed
Summary
This summary is machine-generated.

We developed a quantum-centric supercomputing workflow to calculate molecular electronic structure for large proteins. This method accurately predicts energies of protein conformers using quantum hardware and wave function-based embedding.

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Area of Science:

  • Quantum computing
  • Computational chemistry
  • Molecular modeling

Background:

  • Accurate electronic structure calculations are crucial for understanding molecular behavior.
  • Simulating large biomolecules like proteins is computationally demanding.
  • Fragment-based methods offer a potential solution for scaling quantum chemistry calculations.

Purpose of the Study:

  • To implement and evaluate a quantum-centric supercomputing workflow for molecular electronic structure.
  • To predict the relative energies of two conformers of the 303-atom Trp-cage miniprotein.
  • To assess the accuracy and impact of fragmentation on large-scale quantum chemical calculations.

Main Methods:

  • Utilized a fragment-based, quantum-centric supercomputing workflow.
  • Employed extended wave function-based embedding (EWF) with explicit inclusion of all atoms.
  • Applied sample-based quantum diagonalization (SQD) for complex fragments and full configuration interaction (FCI) for simpler ones.
  • Compared EWF-(FCI,SQD) results with EWF-MP2, EWF-CCSD, RI-MP2, and DLPNO-CCSD benchmarks.

Main Results:

  • The EWF-(FCI,SQD) workflow successfully predicted relative energies for Trp-cage conformers.
  • Fragmentation impact on relative energies was evaluated against unfragmented calculations.
  • Demonstrated feasibility of large-scale electronic configuration interaction (CI) simulations for proteins.

Conclusions:

  • The implemented quantum-centric workflow enables accurate electronic structure calculations for large biomolecules.
  • Combining quantum and classical computing resources is effective for tackling complex protein simulations.
  • This approach paves the way for advanced computational studies of biological systems.