Welcome to QuantumBio Structure Preparation and Refinement Services

Save time and achieve precision results with QuantumBio’s expert team at your side. We’re here to streamline your research efforts and deliver the results you need promptly. Whether you need to augment your team, validate your ideas, or meet research milestones, QuantumBio has the solutions for you.

  • Augment your team: No need to hire additional staff. QuantumBio can collaborate with your team, understand your goals, and deliver the results you require.
  • Test your ideas: Our Standard Service generally ensures that you receive results in a week or less (from the time we receive the structure, executed agreement, and accepted quote).
  • Achieve research milestones: If you have a project meeting approaching or require highly accurate structures for structure-based drug discovery, molecular dynamics, lead optimization, or medicinal chemistry campaigns, our Rush Service is available.
  • 10% Discount to current Licensees: Already a QuantumBio software licensee? Enjoy a 10% discount on our services.

Get Started Today

To get started, request a quote today. Choose from several agreement options including submitting your own Master Services Agreement (MSA) for consideration or to using our “plain vanilla” QB-MSA available for self-signature. If you’re a member of the Science Exchange Platform, feel free to request a quote through their Marketplace.

Contact Us for more information or review our services below.

Structure Preparation and X-ray / Cryo-EM Refinement & XModeScore

Augment your structural biology efforts with QuantumBio. Whether you collaborate with external CROs or use internal resources, our team is ready to tackle challenging structural problems.

Expanding on the remarkable success of our QM/MM-based X-ray/cryo-EM refinement software suite, which harnesses experimental density in conjunction with the most precise functionals and a built-in real-space refinement engine, QuantumBio excels at generating complete crystal structures that are both chemically and experimentally accurate. Our comprehensive solution draws on our exclusive expertise in protonation state enumeration, flip/rotamer sampling, and mixed-QM/MM Hamiltonian algorithms, complemented by our patented XModeScore technology.

Request Quote

Utilizing these techniques alongside the experimental density you provide, we thoroughly prepare and optimize a range of structures, including protein:ligand, protein:protein, or mixed-protein:DNA (or RNA) biounits*, using state-of-the-art tools and methods.

What’s more, if you lack X-ray or cryo-EM experimental density, rest assured, as we can perform most analyses without it as well. Plus, when we perform the work, the “license” to QuantumBio software is included!

QuantumBio’s state-of-the art, Structure Refinement and Optimization solutions (all using experimental density to verify and score the final models) include:
  • Structure Preparation: We handle protonation and refinement, ensuring chemically accurate crystal structures.
  • Density-Driven Protomer/Tautomer Analysis: Our patented XModeScore methods ensure accurate protonation states.
  • Stereoisomer Characterization: Resolve uncertainties about bound stereoisomers.
  • Flip-State Validation: Discriminate between carbon, nitrogen, and oxygen states with precision.
  • Fragment Bound-Conformer Scoring: Select the best positions for low molecular weight compounds.
  • Protonation and Hydrogen Bond Optimization: Our process uses all-atom refinement and doesn’t rely on “riding protons.”
  • Cutting-Edge Real-Space Refinement: We use advanced linear-scaling QM, MM, and QM/MM techniques, avoiding outdated stereochemical restraints.
  • Final Structures Ready to Go: Delivering complete biounits*, updated PDB, mmCIF, MOL2 coordinate files, and MTZ density files.

Our resulting models are accurate and ready for use in your structure-based drug discovery (SBDD), fragment-based drug discovery (FBDD), lead optimization, and computer-aided drug discovery (CADD) campaigns.

Required Input: Provide a PDB, mmCIF, or MOL2 formatted protein:ligand complex file with the likely ligand/fragment binding mode or modes. Include MTZ, SF.CIF, CCP4 files with available density for X-ray/cryo-EM QM/MM refinement and subsequent analysis.

Optional Services: For a small surcharge, QuantumBio staff can perform ligand docking as required. If you have multiple ligands, cofactors, or copies to score, we can handle that too.

*Note: Accurate BIOMT1 records in the customer-provided PDB/mmCIF file are required for the production of an accurate biounit. In the absence of such records, the analyses will be performed based on the presented atoms and chains.

Ready to elevate your research? Request a quote today and experience the QuantumBio advantage.

Request Quote