Peptide Folding Simulation Service
Peptide folding is critical in biomedicine and molecular design, as it directly governs structure and function, making it a pivotal factor in drug development, antibacterial mechanism research, and disease treatment. As a leader in computational biology, CD ComputaBio has launched peptide folding simulation services with many years of technical accumulation and cutting-edge algorithms and is committed to providing high-precision and high-efficiency molecular dynamics simulation solutions for global scientific research institutions and pharmaceutical companies.
Introduction to Peptide Folding Simulation
Peptide folding simulation, bridging sequence and conformation, advances through collaboration between computational biology and experimental technology. Peptide folding simulation has evolved from simple coarse-grained models to multi-scale approaches integrating force fields and machine learning, revealing the physical and chemical nature of folding and promoting the development of drug design, disease mechanism analysis, and synthetic biology.
Fig 1. Workflow for benchmarking AlphaFold2 on peptide structure prediction. (McDonald E F, et al., 2023)
Hierarchical Strategies for Multi-scale Peptide Folding Simulation
To balance computational accuracy and efficiency, peptide folding simulation uses multi-scale strategies from all-atom to coarse-grained:
Utilize All-Atom Force Fields
Accurately characterize non-bonded interactions between atoms (van der Waals forces, electrostatics, hydrogen bonds), suitable for mechanism analysis of microsecond folding trajectories (such as folding free energy surface calculation of Trp-cage mini-proteins).
Construct Coarse-Grained Models
Simplify multiple atoms into a single "bead", and significantly improve sampling efficiency, especially for long peptides (such as transmembrane domains) or multi-domain protein folding studies in membrane environments (such as multi-helix cooperative folding of lysozyme).
Employ Enhanced Sampling Methods
Overcome the energy barrier crossing problem by modifying the potential energy function or parallel multi-temperature simulation. For example, replica exchange Gaussian accelerated molecular dynamics (REX-GaMD) can simultaneously capture folding intermediates and transition states, revealing the folding-unfolding equilibrium of peptides.
Our Services
CD ComputaBio delivers expert peptide folding simulation services, tailored to the specific needs of academic, biotechnology, and pharmaceutical researchers. CD ComputaBio enables clients to advance their understanding of peptide behavior and functionality through advanced computational solutions.
Types of Peptides
CD ComputaBio provides comprehensive peptide folding simulation services to global clients, addressing the full range from short bioactive peptides to intricate signal peptides. Its expertise delivers high-precision results, enabling clients to optimize drug candidate molecules and analyze conformational changes in disease-related peptides.
- Linear Peptide Folding Simulation
- Branched Peptide Folding Simulation
- More
Methods for Peptide Folding Simulation
CD ComputaBio integrates multiple methods to ensure reliable peptide folding simulations because we understand that technology integration and systematic methods are crucial. CD ComputaBio helps clients overcome challenges in low conformational sampling efficiency and insufficient environmental modeling accuracy.
The Process of Peptide Folding Simulation Service
Customer Inquiry
CD ComputaBio engages with our clients to understand their specific research goals and design a customized simulation plan tailored to their needs.
01
Project Design
CD ComputaBio collects the necessary data and prepare it for simulation, ensuring accuracy and reliability throughout the process.
02
Project Execution
The team of CD ComputaBio conducts advanced simulations using cutting-edge software and algorithms, followed by in-depth analysis to extract meaningful insights.
03
Result Delivery
CD ComputaBio delivers comprehensive reports detailing the results of the simulations, along with expert interpretation and recommendations for further research or development.
04
Our Advantages
- Advanced Algorithms and Software
Using internationally recognized tools such as Amber, GROMACS, and CHARMM, supporting GPU acceleration and large-scale parallel computing.
- Multi-scale Modeling Capabilities
From all-atom force fields (such as AMBER) to coarse-grained models (such as MARTINI), adapting to different accuracy requirements.
- Customized Services
Adjust parameters (such as temperature, pressure, solvent ion strength) according to customer needs and provide personalized analysis solutions.
Peptide folding is a pivotal process that influences a myriad of biological functions and therapeutic applications. CD ComputaBio is committed to advancing your research with our specialized peptide folding simulation services. Our extensive expertise, state-of-the-art technology, and collaborative approach ensure that you gain valuable insights into peptide dynamics and folding mechanisms. If you are interested in our services or have any questions, please feel free to contact us.
Reference:
- McDonald E F, Jones T, Plate L, et al. Benchmarking AlphaFold2 on peptide structure prediction[J]. Structure, 2023, 31(1): 111-119. e2.
* For Research Use Only.
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