Computer Aided Drug Design Service

Computer-aided drug design is important for new drug research. It is based on computational chemistry and is a method of designing and optimizing lead compounds through computer simulation, calculation and budgeting of the relationship between drugs and receptor biomacromolecules. Computer-aided drug design generally includes active site analysis, database search, and new drug design.

Figure 1. Computer Aided Drug Design Service.

Method

• Forward screening

It is a process of finding potential compounds based on known targets. According to the screening principle, forward screening can be divided into two categories, namely virtual screening based on molecular docking and virtual screening based on pharmacophore.

• Reverse screening

Reverse virtual screening is a process of finding potential drug targets for a given drug or small active molecule through computational methods. On the basis of the target database, CD ComputaBio has successfully built a reverse virtual screening service platform to provide customers with compound target confirmation, drug new action research, drug toxicity and side effects research services, and provide target-related PubMed, EC, UniProt. CAS , DrugBank drug chemical information and target active site information search.

Overall solutions

• Molecular Dynamics Simulation (MD).
• Homology Modeling/Homology Modeling.
• Structure-based Drug Design.
• Fragment-based Drug Design.
• De novo Design.
• Multiple Targeting Design.
• Scaffold Replacement.
• Combinatorial Library.
• Structure-activity relationship analysis and modeling (QSAR)

Our services

Related Services:

• Structure-based Virtual Screening (SBVS) Service
• Reverse Virtual Screening
• 2D-QSAR Service
• 3D-QSAR Service

CD ComputaBio' Computer Aided Drug Design Service can significantly reduce the cost and labor of the subsequent experiments. Computer Aided Drug Design Service is a personalized and customized innovative scientific research service. Each project needs to be evaluated before the corresponding analysis plan and price can be determined. If you want to know more about service prices or technical details, please feel free to contact us.

Computer Aided Drug Design Service FAQs

• • Q: What are the conventional methods of computer aided drug design?

    • A: Our computer-aided drug design approaches include:

      Target-based structural drug design

      Molecular docking, including high-throughput virtual screening program Libdock, precision docking program CDOCKER, fully flexible docking program Flexible Docking; analog 3D binding conformation generation; new drug design, me too/me better drug design, fragment-based ab initio drug design, etc.

      Ligand-based drug design section

      Backbone leap; fragment growth; ligand-based pharmacophore design; ligand-receptor complex-based pharmacophore design; compound database construction and screening; pharmacophore database construction and preservation; reverse target finding based on pharmacophore database; quantitative conformational relationship (QSAR/QSPR) construction and analysis; virtual combinatorial chemical library design and analysis; small molecule-like drug screening; compound conformation search and analysis of compound ADMET and toxicity prediction, etc.

  • Q: What services can you provide in computer aided drug design?

    • A: We offer the following results delivery depending on the service:

      Molecular docking results

      Molecular docking scoring

      Virtual screening results

      Molecular dynamics simulation results

      Molecular dynamics results analysis
  • Q: What type of data will I receive?

    • A: We will send you raw data of docking results, trajectory files of analyzed kinetic simulations, optimized protein structures (pdb files), data analysis results and related image analysis, result analysis, etc.

  • Q: Why we choose CD ComputaBio?

    • A: We have multiple services for experimental biologists, medicinal chemists, structural biologists, computational biologists, and computational chemists in the life sciences. Our services are mainly applied to research areas such as protein structure-function studies, drug discovery, enzyme engineering, food science, and environmental toxicology studies. Through a high-quality graphical interface, scientific algorithms validated over many years, and an integrated environment, we provide scientists with easy-to-use computational simulation tools to help research in the life sciences, which can reduce costs, shorten cycles, improve efficiency, and explain experimental phenomena.

  • Q: What can you do with computer aided drug design?

    • A:

      Combination mode prediction

      Study/predict the interaction between active small molecules and biomolecules/nanomaterials, analyze the mode of action, and explore the catalytic mechanism of action initially.

      High-throughput virtual screening

      Quickly find potentially active small molecules from compound database, save experimental cost and improve hit rate.

  • Q: How to conduct ab initio design?

    • A: The ab initio design method generally consists of five processes:

      Obtaining the three-dimensional structure of the receptor and its active site.

      Calculating the structural properties of the active site.

      Setting up matching atoms or groups at key active sites

      Generating complete molecules on the basis of the original groups or linking the above atoms or groups into complete molecules with linking groups.

      Ppredicting the affinity of the designed series of compounds to the target site, etc., respectively.
  • Q: What is the principle of computer-aided drug design?

    • A: The general principle of computer-aided drug design is to first obtain the structure of the binding site of the receptor macromolecule by techniques such as X-single crystal diffraction techniques, and to analyze the structural properties of the binding site, such as electrostatic field, hydrophobic field, hydrogen bonding site distribution, and other information using molecular simulation software. Then, using database search or new drug molecule design techniques, molecules with molecular shape and physicochemical properties matching the receptor site are identified, synthesized and tested for biological activity, and after several rounds, new lead compounds can be discovered. Thus, computer-aided drug design broadly includes active site analysis, database search, and new drug design.

  • Q: What are the methods of pharmacophore identification?

    • A:
      1. Molecular conformational analysis and molecular stacking. Each molecule in the training set is subjected to conformational analysis, and the lowest energy conformation and other reasonable conformations are searched and stored in the database. Then the conformations of all molecules are superimposed according to certain rules, and the superimposed results are diverse due to different superimposition methods.
      2. Calculate the three-dimensional pharmacophore model. Based on the superposition, the computer can identify the common structural patterns of compounds belonging to the same active level and establish the three-dimensional pharmacophore model of the molecule.
      3. Make the necessary and reasonable corrections to the pharmacophore model.
      4. Apply the pharmacophore model for rational new drug design and virtual screening.

• Natural Medicine Reverse Targeting Service
• Target Prediction Service
• R-group Decomposition Service
• Drug Repositioning Service
• ADC Payloads Synthesis Service
• ADC Antibody Screening