Computer-aided PROTAC Molecular Design

CADD has become increasingly important for PROTAC design as the accuracy of theoretical models has improved. It can screen the most promising PROTAC molecules for specific targets and E3 ligases in a relatively short period of time, saving experimentalists a lot of testing time and capital costs. Our computer-aided drug design (CADD) platform adopts a new strategy in PROTAC molecule design, combining the strategies reported in the literature for CADD design of PROTAC molecules with our own molecular dynamics sampling technology to further improve the accuracy of the calculation results to help design optimized PROTAC molecules, thus increasing the success rate of PROTAC molecule design.

Services Process

  • We obtain warhead and E3 ligand by structure-based ligand design, and then analyze to derive the binding mode of target protein and warhead, and finally determine the possible binding site and mode of linker and warhead.
  • The site and mode of binding of linker to E3 ligand is also available by the same means. We selected various the most representative linker compounds, from which we selected the linker that could generate a stable warhead-linker-ligand combination (i.e., PROTAC molecule), followed by the linker that could obtain a stable conformation of the target-PROTAC-ligase ternary complex. We used it as an alternative molecule to carry out further experimental validation.
  • For the conformational analysis of the target-PROTAC-ligase ternary complex, we can use different strategies, such as using the strategy of studying target-PROTAC first and then target-PROTAC-ligase, or studying target-PROTAC-ligase directly.


Computer-aided PROTAC Molecular Design

At CD ComputaBio, we use a variety of software tools and algorithms to perform computer-aided PROTAC molecular design. Some of the key solutions we offer include:

  • Quantum mechanical (QM) calculations: We use quantum mechanical calculations to simulate the electronic structure and properties of molecules at the quantum level. Our team can use QM calculations to study the reactivity of potential PROTAC molecules and to predict their pharmacokinetic and toxicological properties.
  • Machine Learning: We use machine learning algorithms to analyze molecular data and predict the activity, selectivity, and toxicity of potential drug candidates. Our team can use these techniques to optimize the design of E3 ligase conjugates, target protein conjugates, and linkers in PROTAC molecules.


  • Compound library screening
  • Customized PROTAC molecules
  • Modular design of PROTAC molecules
  • Activity assays
  • Structure determination
  • Accurate and reproducible results

Why Choose Us?

CD ComputaBio is a leading provider of computer-aided PROTAC molecular design. Our team of experienced computational chemists uses state-of-the-art technology and software tools to create efficient and effective drug molecules. Through our services, we can help you overcome the challenges associated with traditional drug development methods and accelerate your path to clinical success.

* For Research Use Only.