Umbrella Sampling Simulation Service

Umbrella sampling simulation is a molecular dynamics simulation method for calculating the free energy difference of a molecule under a complex potential energy surface. The method guides a molecule from one state to another by applying an applied potential field, and the free energy difference between the two states is obtained by calculating the potential energy difference corresponding to the applied potential field. This technique is particularly important in the study of protein-ligand binding, protein-protein interactions, and membrane permeation processes. This technique yields indispensable data concerning the potential energy of proteins, the behavior of biomolecules, and pathways of biological reactions. As a global leaders in the field of computer-aided drug design, CD ComputaBio provides expert umbrella sampling simulation services.

Our Service

01

Free Energy Calculation

We provide precise computation of free energy variations related to protein-ligand interactions, helping predict the affinity of potential drug candidates.

02

Reaction Pathway Study

Our simulations help map potential energy surfaces and identify optimum reaction pathways, leading to insights for enzyme catalysis and reaction mechanisms.

03

Data Analysis and Interpretation

Beyond conducting simulations, we offer comprehensive data analysis services to extract meaningful conclusions from simulation results. We employ statistical methods and visualization techniques to elucidate the underlying mechanisms governing molecular interactions

Force Fields in Umbrella Sampling Simulation

CHARMM Force Field

Our implementation of the CHARMM force field enables accurate and reliable simulations of biomolecular systems, capturing intricate details of molecular interactions and dynamics. By incorporating CHARMM parameters, we enhance the predictive power of our simulations and refine the structural modeling of proteins.

AMBER Force Field

The AMBER force field, renowned for its versatility and robustness, underpins our molecular dynamics simulations with high-fidelity energy calculations and force evaluations. By utilizing AMBER parameters, we ensure the accuracy and consistency of our simulations, enabling comprehensive analyses of protein-ligand interactions.

GROMACS Force Field

We have facilitated efficient simulations of biomolecular systems using the GROMACS force field to explore complex molecular dynamics. By leveraging the GROMACS algorithm, we have accelerated simulations and enhanced our understanding of protein behavior in different cellular environments.

Sample Requirements

To ensure accurate and reliable simulation results, we require all samples to be prepared according to specific guidelines. These include:

Protein Sequence

The amino acid sequence representation of the protein.

Ligand Information

If studying protein-ligand interactions, provide comprehensive details of ligand.

System Information

Details on the environmental conditions and intended reaction mechanism.

Result Analysis Services

Umbrella Sampling Simulation

Umbrella Sampling Simulation

Reaction Pathway Study

Reaction Pathway Study

Stability Analysis

Stability Analysis

Free Energy Calculation

Free Energy Calculation

Results Delivery

Upon completion of umbrella sampling simulation, we provide a comprehensive results package which includes detailed simulation protocols, raw simulation data, and the calculated Potential of Mean Force (PMF). Our team of experts is available to explain the results and clarify any questions you may have regarding the simulation findings.

Our Advantages

Our Advantages

Expertise and Experience

Our team comprises seasoned computational biologists, bioinformaticians, and molecular modeling experts with a wealth of experience in conducting Umbrella Sampling Simulations. We offer unparalleled expertise in designing and executing simulations tailored to diverse research needs.

Our Advantages

Cutting-edge Technologies

At CD ComputaBio, we leverage state-of-the-art computational tools and high-performance computing resources to deliver reliable and insightful Umbrella Sampling Simulation services. We ensure that our clients benefit from innovative approaches and robust methodologies in their research endeavors.

Our Advantages

Quality Assurance

Quality assurance is at the core of our service ethos at CD ComputaBio. We adhere to stringent quality control measures throughout the simulation process, from initial setup to data analysis, to guarantee the accuracy, reproducibility, and reliability of our results.

At CD ComputaBio, we are committed to providing top-notch computational biology services that contribute significantly to the field of drug design and discovery. Contact us today to get started on your umbrella sampling simulation demands.

Reference:

  1. Bekker G J, Fukuda I, Higo J, et al. Mutual population-shift driven antibody-peptide binding elucidated by molecular dynamics simulations. Scientific Reports, 2020, 10(1): 1406.
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