Molecular docking in an easy way

You focus on chemical insights; we handle the technical challenges.

Molecular docking is a key initial step in computer-aided drug design (CADD), where a candidate drug is inserted into a protein's binding pocket to predict its best binding pose. However, docking prioritizes speed over accuracy, often performing worse than force-field-based methods. Instead of direct interaction strength, docking results are evaluated using a 'score.'

Various search and scoring algorithms improve docking accuracy, including:

• Flexible Receptor: Considers multiple protein conformations, crucial for hidden binding sites.

• Hydrated Docking: Includes water molecules to enhance hydrogen bonding interactions.

• Covalent Docking: Accounts for covalent bond formation, as seen in Nirmatrelvir (COVID-19 inhibitor).

Docking is not a single step but a complex workflow requiring ligand/receptor preparation and careful configuration. Errors in protonation states, ligand geometry, or charge models can significantly alter results.

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For making the molecular docking easier, especially for biologists without the training in computational chemistry, we provide an integrated platform with user-friendly UI for docking. The user only needs to upload their drugs and protein, and check their structure. Click some buttons, the tasks will be finished.

Fig 1. Docking workflow.

We also provided an advanced analysis panel for users. By using Molstar package, we can provide publish-level graphs.

Fig 2. Advanced Docking analysis

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Many platforms offer user-friendly docking services, but why choose ours?

If you need isomer searching or geometry optimization before docking, switching between programs and transferring files can be tedious. Our workflow UI simplifies this by seamlessly integrating complex, customizable workflows—like pre-optimizing ligands with semi-empirical methods before docking.

Fig 3. Add geometry optimization into the workflow

Let’s try a more complex workflow, you can fold the protein into the target receptor and add Hydrogen atoms to it. Then optimized the ligand structures. Finally do the docking. All of them can be composed in one workflow.

Fig 4. ESMfold predicts the protein and then perform the docking

Please check the following demo video for details.

If you want to use our platform, please visit our product page.

https://www.quantabricks.xyz/

We are also seeking corporations with startup biomedical companies. We can also provide free services for building your CADD pipeline. Please contact us at,

https://www.quanta-bricks.com/