The free energy landscape (FEL) calculation is obtained by sampling trajectories starting from different peptide conformations. It shows the valleys and hills of free energy experienced by the peptide throughout the simulation. In addition, in the docking calculation FEL becomes more meaningful when a representative structure needs to be chosen. FEL represents a mapping from all possible conformations that a molecule undergoes during a simulation to the corresponding energies. A typical energy is the Gibbs free energy. Therefore, FEL It is usually expressed using two variables, which reflect specific properties of the system and characterize conformational changes. CD BioSciences use computer-aided methods to provide free energy landscape analysis of biofilm system to help customers complete biofilm related research.

Our Services

CD BioSciences provides one-stop free energy landscape analysis service of biofilm system. We offer a variety of methods and software to choose from to meet your research needs.

Specific Free Energy Landscape Analysis Approaches We Offer

• CD BioSciences use the GROMACS command sham to calculate the FEL. For a better experience, we provide some additional scripts and display them directly.
• We will calculate two variables to represent the free energy. To represent the conformational change of the polypeptide, we calculate its radius of gyration, and the RMSD relative to the mean structure.
• We do not use the native state because that would disrupt subsequent docking simulations. Also, we can compute these variables based on the merged trajectories. A prerequisite for computing the FEL is adequate sampling, or repeating long simulations with different initial velocities, or As we have done, start the simulation from a different conformation.

Provided by Clients

Please inform us of your specific free energy landscape analysis of biofilm system details, and we can provide customized solutions for different projects.

Service Process

Our Features

Deliverables

1. Related experimental results raw data
2. Analysis results of free energy landscape
3. Experimental report
4. Data analysis
5. Image and result analysis
6. Summary of relevant calculation parameters

Why Choose Us?

CD BioScience is a well-known nanocage service provider and supports most of the biofilm related services. CD BioScienceis is committed to improving various biofilm related services. We are able to design and complete a set of services as solutions for themed projects. Please feel free to contact us for more detailed information, our scientists will tailor the most reasonable plan for your project.

• Biofilm Computational Construction Service
• Biofilm Molecular Dynamics Simulation Service
• Stability Test of Biofilm System
• RMSF Analysis of Biofilm System
• Gyration Radius Analysis of Biofilm System
• Binding Mode Analysis of Biofilm System
• Secondary Structure Analysis of Biofilm System
• Energy Analysis of Biofilm System
• Hydrophobic Interaction Analysis of Biofilm System
• Biofilm Conformational Principal Component Analysis
• Biofilm Ramachandran Plots Analysis
• Cluster Analysis of Biofilm System
• SAS Analysis Service of Biofilm System
• Energy Decomposition Analysis of Biofilm System
• Electrostatic Interaction Analysis of Biofilm System
• Biofilm Virtual Screening Service
• Computational Modeling of Early-Stage Biofilm Formation
• Biofilm CGMD Service
• Biofilm DPD Service
• Biofilm DEM Service
• Biofilm SPH Service
• Biofilm XFEM Service
• Other Biofilm MD Serivce
• Biofilm Homology Modeling Serivce
• Gram-negative Bacterial Outer Membrane Construction Service
• Biofilm Formation Simulation Service
• Construction Services for Discrete Difference Models
• Modeling Services for Geometric Heterogeneity in Biofilms
• Computational Simulation Service for Biofilm Development
• Computational Modeling Service for Synthetic Biofilms
• Biofilm MD Results Analysis Services
• Biofilm Multiscale Computational Modeling Service
• Biofilm Modeling Service