Challenges
Datasets
Workspaces
Papers
Discussions
Leaderboard
Log inSign up
Challenges
Datasets
Workspaces
Papers
Discussions
Leaderboard
Blog
Job Board
Q3AS

© 2026 Aqora Quantum S.A.S.

TermsPrivacyLegal Notice

Computers in Biology and Medicine

Classical Simulations on Quantum Computers: Interface-Driven Peptide Folding on Simulated Membrane Surfaces

Daniel Conde-Torres, Mariamo Mussa Juane, Daniel Faílde, Andrés Gómez, Rebeca García‐Fandiño, Ángel Piñeiro

Published Sep 24, 2024• 10 citations
Publisher

Abstract

BACKGROUND: Antimicrobial peptides (AMPs) are crucial in the fight against infections and play significant roles in various health contexts, including cancer, autoimmune diseases, and aging. A key aspect of AMP functionality is their selective interaction with pathogen membranes, which often exhibit altered lipid compositions. These interactions are thought to induce a conformational shift in AMPs from random coil to alpha-helical structures, essential for their lytic activity. Traditional computational approaches have faced challenges in accurately modeling these structural changes, especially in membrane environments, thereby opening and opportunity for more advanced approaches. METHOD: This study extends an existing quantum computing algorithm, initially designed for peptide folding simulations in homogeneous environments, to address the complexities of AMP interactions at interfaces. Our approach enables the prediction of the optimal conformation of peptides located in the transition region between hydrophilic and hydrophobic phases, resembling lipid membranes. The new method was tested on three 10-amino-acid-long peptides, each characterized by distinct hydrophobic, hydrophilic, or amphipathic properties, across different media and at interfaces between solvents of different polarity. RESULTS: The developed method successfully modeled the structure of the peptides without increasing the number of qubits required compared to simulations in homogeneous media, making it more feasible with current quantum computing resources. Despite the current limitations in computational power and qubit availability, the findings demonstrate the significant potential of quantum computing in accurately characterizing complex biomolecular processes, particularly AMP folding at membrane models. CONCLUSIONS: This research highlights the promising applications of quantum computing in biomolecular simulations, paving the way for future advancements in the development of novel therapeutic agents. We aim to offer a new perspective on enhancing the accuracy and applicability of biomolecular simulations in the context of AMP interactions with membrane models.

DOI
10.1016/j.compbiomed.2024.109157

Related papers

Interface-Driven Peptide Folding: Quantum Computations on Simulated Membrane Surfaces

Daniel Conde-Torres, Mariamo Mussa Juane, Daniel Faílde +3 more

Antimicrobial peptides (AMPs) play important roles in cancer, autoimmune diseases, and aging. A critical aspect of AMP functionality is their targeted interaction with pathogen membranes, which often possess altered lipid compositions. Designing AMPs with enhanced therapeutic properties relies on a nuanced understanding of these interactions, which are believed to trigger a rearrangement of these peptides from random coil to alpha-helical conformations, essential for their lytic action. Traditional supercomputing has consistently encountered difficulties in accurately modeling these structural changes, especially within membrane environments, thereby opening an opportunity for more advanced approaches. This study extends an existing quantum computing algorithm to address the complexities of antimicrobial peptide interactions at interfaces. Our approach enables the prediction of the optimal conformation of peptides located in the transition region between hydrophilic and hydrophobic phases, akin to lipid membranes. The new method has been applied to model the structure of three 10-amino-acid-long peptides, each exhibiting hydrophobic, hydrophilic, or amphipathic properties in different media and at interfaces between solvents of different polarity. Notably, our approach does not demand a higher number of qubits compared to simulations in homogeneous media, making it more feasible with current quantum computing resources. Despite existing limitations in computational power and qubit accessibility, our findings demonstrate the significant potential of quantum computing in accurately characterizing complex biomolecular processes, particularly the folding of AMPs at membrane models. This research paves the way for future advances in quantum computing to enhance the accuracy and applicability of biomolecular simulations.

arXiv:2401.05075•Jan 10, 2024•1 citation

Capturing Protein Free Energy Landscape using Efficient Quantum Encoding

Kannan, Ashwini, Jaya Vasavi Pamidimukkala, Avinash Dakshinamoorthy +3 more

Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is critical, as a protein's functionality is inherently linked to its final folded form. Misfolding can lead to severe diseases such as Alzheimer's and cystic fibrosis, highlighting the biological and clinical importance of understanding protein folding mechanisms. This work presents a novel turn based encoding optimization algorithm for predicting the folded structures of peptides and small proteins. Our approach builds upon our previous research, where our objective function focused on hydrophobic collapse, a fundamental phenomenon underlying the protein folding process. In this work, we extend that framework by not only incorporating hydrophobic interactions but also including all non bonded interactions modeled using the Miyazawa Jernigan potential. We constructed a Hamiltonian from the defined objective function that encodes the folding process on a three dimensional face centered cubic lattice, offering superior packing efficiency and a realistic representation of protein conformations. This Hamiltonian is then solved using classical and quantum solvers to explore the vast conformational space of proteins. To identify the lowest-energy folded configurations, we utilize the Variational Quantum Eigensolver implemented on IBM 133 qubit hardware. The predicted structures are validated against experimental data using root mean square deviation as a metric and compared against classical simulated annealing and molecular dynamics simulation results. Our findings highlight the promise of hybrid classical and quantum approaches in advancing protein folding predictions, particularly for sequences with low homology.

arXiv:2510.15316•Oct 17, 2025•0 citations

A comparative insight into peptide folding with quantum CVaR-VQE algorithm, MD simulations and structural alphabet analysis

Akshay Uttarkar, Vidya Niranjan

Abstract Quantum computing in biology is one of the most rapidly evolving field of technology. Protein folding is one of the key challenges which requires accurate and efficient algorithms with a quick computational time. Structural conformations of proteins with disordered regions need colossal amount of computational resource to map its least energy conformation state. In this regard, quantum algorithms like Variational quantum eigensolver (VQE) are applied in the current research work to predict the lowest energy value of 50 peptides of 7 amino acids each. VQE is initially used to calculate the energy values over which Variational Quantum Optimization is applied via Conditional Value at Risk (CVaR) over 100 iterations of 500000 shots each to obtain least ground state energy value. This is compared to the molecular dynamics-based simulations of 50 nanoseconds each to calculate the energy values along with the folding pattern. The results suggest efficient folding outcomes from CvaR-VQE compared to MD based simulations. With the ever-expanding quantum hardware and improving algorithms the problem of protein folding can be resolved to obtain in depth insights on the biological process and drug design.

Quantum Information Processing•Feb 6, 2024•8 citations

Resource-efficient quantum algorithm for protein folding

Anton Robert, Panagiotis Kl. Barkoutsos, Stefan Woerner +1 more

Abstract Predicting the three-dimensional structure of a protein from its primary sequence of amino acids is known as the protein folding problem. Due to the central role of proteins’ structures in chemistry, biology and medicine applications, this subject has been intensively studied for over half a century. Although classical algorithms provide practical solutions for the sampling of the conformation space of small proteins, they cannot tackle the intrinsic NP-hard complexity of the problem, even when reduced to the simplest Hydrophobic-Polar model. On the other hand, while fault-tolerant quantum computers are beyond reach for state-of-the-art quantum technologies, there is evidence that quantum algorithms can be successfully used in noisy state-of-the-art quantum computers to accelerate energy optimization in frustrated systems. In this work, we present a model Hamiltonian with $${\mathcal{O}}({N}^{4})$$ O ( N 4 ) scaling and a corresponding quantum variational algorithm for the folding of a polymer chain with N monomers on a lattice. The model reflects many physico-chemical properties of the protein, reducing the gap between coarse-grained representations and mere lattice models. In addition, we use a robust and versatile optimization scheme, bringing together variational quantum algorithms specifically adapted to classical cost functions and evolutionary strategies to simulate the folding of the 10 amino acid Angiotensin on 22 qubits. The same method is also successfully applied to the study of the folding of a 7 amino acid neuropeptide using 9 qubits on an IBM 20-qubit quantum computer. Bringing together recent advances in building gate-based quantum computers with noise-tolerant hybrid quantum-classical algorithms, this work paves the way towards accessible and relevant scientific experiments on real quantum processors.

arXiv:1908.02163•npj Quantum Information•Feb 17, 2021•202 citations

Protein Structure Prediction with High Degrees of Freedom in a Gate-Based Quantum Computer

Jaya Vasavi Pamidimukkala, Soham Bopardikar, Avinash Dakshinamoorthy +3 more

Protein folding, which traces the protein three-dimensional (3D) structure from its amino acid sequence, is a half-a-century-old problem in biology. The function of the protein correlates with its structure, emphasizing the need to study protein folding to understand the cellular and molecular processes better. While recent AI-based methods have shown significant success in protein structure prediction, their accuracy diminishes with proteins of low sequence similarity. Classical simulations face challenges in generating extensive conformational samplings. In this work, we develop a novel turn-based encoding algorithm with more significant degrees of freedom that successfully runs on a gate-based quantum computer and predicts the structure of proteins of varied lengths utilizing up to 114 qubits (IBM hardware). To make the problem tractable in quantum computers, the protein sequences were described with the simplistic HP model (H = hydrophobic residues, P = polar residues). The proposed formulation successfully captures the so-called nucleation step in protein folding, the hydrophobic collapse, that brings the hydrophobic residues to the core of the protein.

arXiv:2311.14141•Journal of Chemical Theory and Computation•Nov 6, 2024•9 citations

Quantum Algorithmic Approaches to Protein Folding: A Comprehensive Study of Diverse Lattice Structures

Venugopal K, Anagha Muralidharan, Cherishma Kumar Subhasa +2 more

In computational biology, protein folding continues to be a key challenge with important implications for drug design and biological function comprehension. Using both classical and quantum computing methods, this paper provides an in-depth analysis of various possible lattice configurations and how theyare used in protein folding. To assess the protein design, we investigate classic models including the more intricate Miyazawa-Jernigan (MJ) interaction matrix and the hydrophobic-hydrophilic (HP) lattice model. Furthermore, we use integer programming methods to protein folding problems on lattices, addressing their NP-hardness and proving their effectiveness in obtaining optimal solutions. Expanding upon these conventional techniques, we present sophisticated graph neural network (GNN) models, particularly the RG-MPNN, which integrate pharmacophore ideas to predict chemical properties by using task-related representations. In the latter section of our paper, we examine how protein folding simulations on lattice structures could be transformed using quantum algorithms. Compared to classical methods, quantum computational techniques promise to be more accurate and efficient at handling the enormous diversity and complexity of protein folding.

International Conference on Computation System and Information Technology for Sustainable Solutions (CSITSS)•Nov 7, 2024•1 citation
BACKGROUND: Antimicrobial peptides (AMPs) are crucial in the fight against infections and play significant roles in various health contexts, including cancer, autoimmune diseases, and aging. A key aspect of AMP functionality is their selective interaction with pathogen membranes, which often exhibit altered lipid compositions. These interactions are thought to induce a conformational shift in AMPs from random coil to alpha-helical structures, essential for their lytic activity. Traditional computational approaches have faced challenges in accurately modeling these structural changes, especially in membrane environments, thereby opening and opportunity for more advanced approaches. METHOD: This study extends an existing quantum computing algorithm, initially designed for peptide folding simulations in homogeneous environments, to address the complexities of AMP interactions at interfaces. Our approach enables the prediction of the optimal conformation of peptides located in the transition region between hydrophilic and hydrophobic phases, resembling lipid membranes. The new method was tested on three 10-amino-acid-long peptides, each characterized by distinct hydrophobic, hydrophilic, or amphipathic properties, across different media and at interfaces between solvents of different polarity. RESULTS: The developed method successfully modeled the structure of the peptides without increasing the number of qubits required compared to simulations in homogeneous media, making it more feasible with current quantum computing resources. Despite the current limitations in computational power and qubit availability, the findings demonstrate the significant potential of quantum computing in accurately characterizing complex biomolecular processes, particularly AMP folding at membrane models. CONCLUSIONS: This research highlights the promising applications of quantum computing in biomolecular simulations, paving the way for future advancements in the development of novel therapeutic agents. We aim to offer a new perspective on enhancing the accuracy and applicability of biomolecular simulations in the context of AMP interactions with membrane models.
Antimicrobial peptides (AMPs) play important roles in cancer, autoimmune diseases, and aging. A critical aspect of AMP functionality is their targeted interaction with pathogen membranes, which often possess altered lipid compositions. Designing AMPs with enhanced therapeutic properties relies on a nuanced understanding of these interactions, which are believed to trigger a rearrangement of these peptides from random coil to alpha-helical conformations, essential for their lytic action. Traditional supercomputing has consistently encountered difficulties in accurately modeling these structural changes, especially within membrane environments, thereby opening an opportunity for more advanced approaches. This study extends an existing quantum computing algorithm to address the complexities of antimicrobial peptide interactions at interfaces. Our approach enables the prediction of the optimal conformation of peptides located in the transition region between hydrophilic and hydrophobic phases, akin to lipid membranes. The new method has been applied to model the structure of three 10-amino-acid-long peptides, each exhibiting hydrophobic, hydrophilic, or amphipathic properties in different media and at interfaces between solvents of different polarity. Notably, our approach does not demand a higher number of qubits compared to simulations in homogeneous media, making it more feasible with current quantum computing resources. Despite existing limitations in computational power and qubit accessibility, our findings demonstrate the significant potential of quantum computing in accurately characterizing complex biomolecular processes, particularly the folding of AMPs at membrane models. This research paves the way for future advances in quantum computing to enhance the accuracy and applicability of biomolecular simulations.
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is critical, as a protein's functionality is inherently linked to its final folded form. Misfolding can lead to severe diseases such as Alzheimer's and cystic fibrosis, highlighting the biological and clinical importance of understanding protein folding mechanisms. This work presents a novel turn based encoding optimization algorithm for predicting the folded structures of peptides and small proteins. Our approach builds upon our previous research, where our objective function focused on hydrophobic collapse, a fundamental phenomenon underlying the protein folding process. In this work, we extend that framework by not only incorporating hydrophobic interactions but also including all non bonded interactions modeled using the Miyazawa Jernigan potential. We constructed a Hamiltonian from the defined objective function that encodes the folding process on a three dimensional face centered cubic lattice, offering superior packing efficiency and a realistic representation of protein conformations. This Hamiltonian is then solved using classical and quantum solvers to explore the vast conformational space of proteins. To identify the lowest-energy folded configurations, we utilize the Variational Quantum Eigensolver implemented on IBM 133 qubit hardware. The predicted structures are validated against experimental data using root mean square deviation as a metric and compared against classical simulated annealing and molecular dynamics simulation results. Our findings highlight the promise of hybrid classical and quantum approaches in advancing protein folding predictions, particularly for sequences with low homology.
Abstract Quantum computing in biology is one of the most rapidly evolving field of technology. Protein folding is one of the key challenges which requires accurate and efficient algorithms with a quick computational time. Structural conformations of proteins with disordered regions need colossal amount of computational resource to map its least energy conformation state. In this regard, quantum algorithms like Variational quantum eigensolver (VQE) are applied in the current research work to predict the lowest energy value of 50 peptides of 7 amino acids each. VQE is initially used to calculate the energy values over which Variational Quantum Optimization is applied via Conditional Value at Risk (CVaR) over 100 iterations of 500000 shots each to obtain least ground state energy value. This is compared to the molecular dynamics-based simulations of 50 nanoseconds each to calculate the energy values along with the folding pattern. The results suggest efficient folding outcomes from CvaR-VQE compared to MD based simulations. With the ever-expanding quantum hardware and improving algorithms the problem of protein folding can be resolved to obtain in depth insights on the biological process and drug design.
Abstract Predicting the three-dimensional structure of a protein from its primary sequence of amino acids is known as the protein folding problem. Due to the central role of proteins’ structures in chemistry, biology and medicine applications, this subject has been intensively studied for over half a century. Although classical algorithms provide practical solutions for the sampling of the conformation space of small proteins, they cannot tackle the intrinsic NP-hard complexity of the problem, even when reduced to the simplest Hydrophobic-Polar model. On the other hand, while fault-tolerant quantum computers are beyond reach for state-of-the-art quantum technologies, there is evidence that quantum algorithms can be successfully used in noisy state-of-the-art quantum computers to accelerate energy optimization in frustrated systems. In this work, we present a model Hamiltonian with O(N4){\mathcal{O}}({N}^{4})O(N4) O ( N 4 ) scaling and a corresponding quantum variational algorithm for the folding of a polymer chain with N monomers on a lattice. The model reflects many physico-chemical properties of the protein, reducing the gap between coarse-grained representations and mere lattice models. In addition, we use a robust and versatile optimization scheme, bringing together variational quantum algorithms specifically adapted to classical cost functions and evolutionary strategies to simulate the folding of the 10 amino acid Angiotensin on 22 qubits. The same method is also successfully applied to the study of the folding of a 7 amino acid neuropeptide using 9 qubits on an IBM 20-qubit quantum computer. Bringing together recent advances in building gate-based quantum computers with noise-tolerant hybrid quantum-classical algorithms, this work paves the way towards accessible and relevant scientific experiments on real quantum processors.
Protein folding, which traces the protein three-dimensional (3D) structure from its amino acid sequence, is a half-a-century-old problem in biology. The function of the protein correlates with its structure, emphasizing the need to study protein folding to understand the cellular and molecular processes better. While recent AI-based methods have shown significant success in protein structure prediction, their accuracy diminishes with proteins of low sequence similarity. Classical simulations face challenges in generating extensive conformational samplings. In this work, we develop a novel turn-based encoding algorithm with more significant degrees of freedom that successfully runs on a gate-based quantum computer and predicts the structure of proteins of varied lengths utilizing up to 114 qubits (IBM hardware). To make the problem tractable in quantum computers, the protein sequences were described with the simplistic HP model (H = hydrophobic residues, P = polar residues). The proposed formulation successfully captures the so-called nucleation step in protein folding, the hydrophobic collapse, that brings the hydrophobic residues to the core of the protein.
In computational biology, protein folding continues to be a key challenge with important implications for drug design and biological function comprehension. Using both classical and quantum computing methods, this paper provides an in-depth analysis of various possible lattice configurations and how theyare used in protein folding. To assess the protein design, we investigate classic models including the more intricate Miyazawa-Jernigan (MJ) interaction matrix and the hydrophobic-hydrophilic (HP) lattice model. Furthermore, we use integer programming methods to protein folding problems on lattices, addressing their NP-hardness and proving their effectiveness in obtaining optimal solutions. Expanding upon these conventional techniques, we present sophisticated graph neural network (GNN) models, particularly the RG-MPNN, which integrate pharmacophore ideas to predict chemical properties by using task-related representations. In the latter section of our paper, we examine how protein folding simulations on lattice structures could be transformed using quantum algorithms. Compared to classical methods, quantum computational techniques promise to be more accurate and efficient at handling the enormous diversity and complexity of protein folding.