Lance Westerhoff from QuantumBio Inc. will give a presentation September 22nd to introduce SBGrid members to the Phenix/DivCon, a tool for accurate macromolecular crystallographic refinement using linear scaling, semiempirical quantum-mechanics.
Phenix/DivCon: accurate macromolecular crystallographic refinement using linear scaling, semiempirical quantum-mechanics
President and General Manager
Host: Jason Key
Conventional, biomolecular crystallographic refinement relies on often dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the X-ray model of the biomolecule and any bound ligand(s) and cofactors. The ligand stereochemical restraint file (CIF) requires an a priori understanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. At the same time, crucial interactions such as hydrogen bonds, electrostatics, and so on are completely absent from the conventional refinement functional. Recently, we have completely replaced these stereochemical restraints with a more robust functional through the integration of the linear-scaling, semiempirical quantum mechanics (SE-QM) program DivCon with the Phenix X-ray refinement engine. Unlike with conventional refinement, Phenix/DivCon does not utilize CIF(s), link restraints and other refinement parameters and hence it allows one to make fewer assumptions about the model. With the addition of accurate energy and density scoring tools, this work has been further expanded to include not only refinement but tautomer/protomer and “flip state” determination as well.
The DivCon plugin to the Phenix package is available within the SBGrid environment and it may be used in non-profit efforts leading to intellectual property released directly into the public domain (separate permission may be obtained in order to generate intellectual property licensed for for-profit use).
Learn more about the Phenix/DivCon plugin on the website.
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