CD BioSciences' homology modeling services can help researchers understand the structural properties of biofilms and can be used for drug screening, discovery of potential disease treatments, or target drug interaction studies. Homology modeling is a practical method for predicting structure from sequences. There are two prerequisites for this approach: the presence of one or several distinguishable structures in the homologous protein of the target sequence, and the high homology of the target sequence to the protein.. CD BioSciences provide one-stop biofilm homology modeling serivce to help customers complete biofilm related research.

Our Service Process

• Template selection and alignment of sequences

We searched protein databases for template proteins with known crystal structures and performed sequence alignments using tools such as BLAST;

• Determine if a template is available

The similarity between the template sequence and the target sequence is >30%;

• Main chain structure construction

Apply the atomic coordinates of the template structure to the target to generate the basic main chain skeleton, and then adjust the atomic positions of the main chain to make the bone structure conform to the stereochemical principle;

• Ring area construction

One approach is to model based on known ring structures. Another way is to predict from scratch based on the principles of quantum chemistry;

• Sidechain modeling and optimization

Use the target sequence fragment to search the rotamer database to obtain similar fragments, then construct the side chain structure of the fragment according to its spatial orientation, and finally perform energy minimization to find the lowest energy point, that is, a stable conformation;

• Overall structure optimization

There are usually unreasonable contacts between atoms in the 3D model obtained by the above process, which need to be eliminated by methods such as simulated annealing and molecular dynamics.

• Structural evaluation

The most commonly used evaluation criterion is RMSD, which represents the root mean square deviation of the corresponding atoms of the target protein and the template protein. It can also be submitted to the SAVES server for verification.

Provided by Customers

Please inform us of your specific biofilm homology modeling serivce details, and we can provide customized solutions for different projects.

Service Process

Our Features

Deliverables

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

Why Choose Us?

CD BioSciences provides professional biofilm homology modeling serivce to meet the needs of regular customers to determine hits on time and on budget. CD BioSciences relies on the world-class technical expertise, we provide customers with the best quality one-stop biofilm service, including the development of experimental procedures according to different experimental needs. 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
• Free Energy Landscape 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
• 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