XModeScore
Unmask Mysterious Protein-Ligand Binding States and Accelerate Structure-based Drug Discovery
Obtain meaningful results in structure-guided drug discovery and structure-based drug discovery. Built on QuantumBio’s structural biology module, you can leverage linear-scaling, semi-empirical, quantum mechanics to generate models with better chemical accuracy—validated against numerous ligands and active sites.
- Accurately determine tautomers, protomers, rotamers, and flip-states using X-ray data — even at low resolution— and fast, quantum mechanics-based, crystallography refinement tools.
- Automatically download coordinates and structure factors directly from the PDB RCSB for preparation and refinement.
- Easily integrate the software into your workflow with our command line accessibility and optional MOE GUI plugin.
- Choose your platform—whether you are using the Phenix suite or the GlobalPhasing BUSTER package, you’ll get the scores you need.
- Optimize your methods and get your questions answered quickly with our team of experts—We are here to help and will get you up and running!
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With XModeScore, you can automatically generate the possible tautomers and structural flip states in a structure and determine the correct protonation pattern and hydrogen bond network for the X-ray model.
Use Case: Human Carbonic Anhydrase II + Acetazolamide (AZM)
XModeScore was challenged with Human Carbonic Anhydrase II + Acetazolamide (AZM) as found in the 1.1 Å PDB X-ray structure 3HS4. This structure has both X-ray data and neutron diffraction data available.
Upon X-ray structure refinement with the X-ray data, we observed a greater amount of +/- density surrounding the AZM in modes 1 and 2—which are the incorrect protonation modes when compared to the neutron diffraction results found in the PDB 4G0C.
The XModeScore results shown in the table for the corresponding protonation modes 1-3 clearly differentiates between the correct mode (i.e. mode 3) and the incorrect modes (i.e. modes 1-2). Read the full publication.
Drive your structure-based drug discovery projects forward by using QuantumBio’s DivCon Discovery Suite—we are constantly improving our platform and are a dedicated collaborator. Our iterative approach delivers software that facilitates better workflows and methods—and most importantly better structures.
If you do not see results comparable to those provided, we want to hear from you so we can support you through the process. Schedule a “virtual visit” to discuss your goals and your chosen protocol.
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It’s Finally Here: X-Ray Crystallography + Computer-Aided Drug Design
A computational chemistry (CADD) ↔ structural biology (X-ray crystallography) “feedback loop”— changing the game in protein:ligand crystallography and structure-based drug design for industrial and academic pharmaceutical researchers.
Publication
XModeScore: a patented method for protonation and flip state determination and binding mode characterization using density analysis coupled with QM/MM refinement.
XModeScore Tutorial
Explore the Phenix/DivCon tutorials to start refining your structures today!
Phenix/DivCon and Buster/DivCon Manuals
Get installation instructions, configuration options, tutorials, and case studies.
DivCon Plugin FAQs
Get your questions answered and learn more about our capabilities in X-ray crystallography.
Guidelines: X-ray Refinement
Learn the key considerations when performing QM-based refinement.