Molecular Docking Service

Overall solution

Our important theoretical models and corresponding docking methods including:

• Lock-and-key model, rigid docking.
• Induced fit model, flexible docking and semi-flexible docking.
• Conformation ensemble model, ensemble docking.

Process of the analysis and docking service

• Structure preparation before docking, including: receptor structure and small molecule compound (library);
• Molecular docking calculation, including: conformation search and scoring evaluation;
• Results analysis, including: docking conformation or seedling compound selection, binding mode analysis, scoring situation and force analysis; etc.

Figure 2. Workflow of molecular docking.

Our molecular docking services

Our molecular docking service mainly focuses on the following two aspects of researches

• Binding mode prediction

Studying the interaction between active small molecules and biological macromolecules and understand their mechanism of action.

• High-throughput virtual screening

Quickly find small molecules with potential activity from the chemical database, save experimental costs and improve the hit rate.

If conditions permit, for binding mode prediction, we need to examine the reproducibility of the combined conformation of the docking software (method), that is, to perform re-dock or self-dock; for high-throughput virtual screening, we need to examine the screening performance, including enrichment rate, goodness of fit. Only through rigorous and scientific processing can we ensure that the simple docking process will get accurate calculation results.

CD ComputaBio also provides you with

• Protein-Small Molecule Docking Service
• Protein-Protein Docking Service
• Reverse Docking Service
• Flexible Peptide Docking
• Protein-DNA Docking Service

CD ComputaBio offers a corresponding molecular docking service. Our molecular docking provides accurate approximations of real molecular behaviors, and have proven to be very useful in understanding the biochemical basis of physiological events at different stages of drug development, even in different fields such as materials science. Our team of experts can provide up to one millisecond of simulation time for the system you choose, so you do not have to worry about technical issues. We can also analyze these results for you. The CD ComputaBio team has been working in this field for more than ten years and has published his findings in top scientific journals.

Molecular Docking Service FAQs

• • Q: What are the molecular docking methods I can choose from?

    • A:

      Rigid docking: The rigid docking method does not change the conformation of the molecules involved in the docking process, but only changes the spatial position and attitude of the molecules. The rigid docking method is the most simplified and has a relatively small computational effort, and is suitable for dealing with docking between large molecules.

      Semi-flexible docking: The semi-flexible docking method allows a certain degree of change in the conformation of small molecules during the docking process, but usually fixes the conformation of large molecules, and the adjustment of the conformation of small molecules may also be limited to a certain extent, such as fixing the bond lengths and bond angles of certain non-critical parts.

      Flexible docking: The flexible docking method allows the conformation of the studied system to change freely during the docking process. Since the variables grow geometrically with the atomic number of the system, the flexible docking method is very computationally intensive and consumes a lot of computer time, which is suitable for the precise examination of intermolecular recognition.

  • Q: What specific molecular docking services can you provide?

    • A: The docking services we can provide include, but are not limited to:

      Protein-small molecule docking services

      Protein-protein docking services

      Reverse docking service

      Flexible peptide docking

      Protein-DNA docking services
  • Q: What is the price of my order?

    • A: For molecular docking services, some accounts can display prices during the order submission process. If this is a feature you are interested in activating, simply contact the CD ComputaBio staff to find out if it is available for your institution. You can also get a quote from our staff.

  • Q: What software can I use to view my results?

    • A: You can use VMD or PyMoL to view the docking results, or you can visualize the proteins and complexes based on the docking results we provide.

  • Q: Why should I choose CD ComputaBio?

    • A: CD ComputaBio is a customer-driven company with operational excellence. We have become a leader in molecular biology services (specifically molecular docking services), offering the best combination of value - fast turnaround, technical expertise, competitive pricing and friendly customer support. We continue to innovate to produce the best results and provide maximum convenience to our customers.

  • Q: What type of data analysis is available?

    • A: Our data analysis includes docking scoring, binding mode analysis and binding free energy analysis.

  • Q: What are the applications of molecular docking?

    • A:

      To explore the specific mode of action and binding conformation of drug small molecules and macromolecular receptors.

      Screening for lead drugs that can bind to their targets (virtual screening).

      Explain the reasons for the activity of drug molecules.

      To guide the rational optimization of drug molecule structures.

• Drug Design Services
• Protein Structure Modeling Service
• Biological Data Analysis
• In Silico Protein-Protein Interactions Prediction Service
• Protein Sequence Analysis Service
• Univariate Analysis