News: QuantumBio Announces the Release of X-ray Crystallography Plug-in for Phenix

We are excited to announce the first public (v1.0) release of our linear scaling, quantum mechanics DivCon Discovery Suite plug-in for X-ray crystallography.

X-ray crystallography is the primary technique used to determine the three-dimensional structure of the protein:ligand and protein:protein complexes that are critical to structure based drug discovery. Conventional X-ray methods often rely on simplified energy functions and user-supplied parameters or restraints to model the protein:ligand and protein:protein complexes that are critical to structure based drug discovery. The DivCon plug-in works in ‘real time’ during the refinement to replace these restraints with a much more rigorous method based on quantum mechanics. This method is able to capture hydrogen-bonding, electrostatics, charge transfer, polarization, and so on – interactions typically overlooked in conventional refinement protocols – in order to more accurately model complexes involving ligands, metal centers, and cofactors. And since our proprietary quantum mechanics implementation scales linearly with the number of atoms, it can be applied not only to the ligand, but also to the surrounding active site and even to the entire complex. For more information on the technique including examples, tutorials, and availability, please see the following link:

http://www.quantumbioinc.com/products/phenix_divcon

DivCon “plugs” into the Python-based Hierarchical ENvironment for Integrated Xtallography (Phenix) platform. Phenix, developed by researchers from Lawrence Berkeley Laboratory, Los Alamos National Laboratory, Duke University, and the University of Cambridge is one of the leading X-ray crystallography suites available. The DivCon integration allows our software to be used within most standard X-ray refinement workflows.

For the past several years, we have been working with industry collaborators in order to validate and prepare this plug-in, and we are excited to release it to the community and bring our advanced computational chemistry tools to the field of X-ray crystallography. This is also the first product to include our new, DivCon6 software, which is 2-5 times faster, exhibits greater parallelism, and is more robust than previous DivCon versions.

The following publications detailing the method are available:

  • Borbulevych, O.Y., J.A. Plumley, R.M. Martin, K.M. Merz Jr, and L.M. Westerhoff, Accurate, macromolecular crystallographic refinement: Incorporation of the linear scaling, semiempirical quantum mechanics program DivCon into the Phenix refinement package. Acta Crystallogr D Biol Crystallogr, 2014. In Press.
  • Borbulevych, O.Y., N.W. Moriarty, P.D. Adams, and L.M. Westerhoff. Quantum Mechanics-based Refinement in Phenix/DivCon. Computational Crystallography Newsletter, 2014. 5: p. 26-30. http://www.phenix-online.org/newsletter/

Our DivCon Discovery Suite integrated with Phenix provides pharmaceutical and biotechnology companies, contract research organizations, consultants, and academic groups with the ability to significantly improve accuracy during structure refinement and the drug discovery processes.

Please look forward to additional announcements regarding further expansion of our DivCon6 software in the near future.

If you have any questions or if you would like to evaluate the software, don’t hesitate to Contact Us or visit the following link:

http://www.quantumbioinc.com/products/software_licensing