All Publications

in year '2014'

July 17, 2014
Computation of the solvation free energy for chemical and biological processes has long been of significant interest. The key challenges to effective solvation modeling center on the choice of potential function and configurational sampling. Herein, an energy sampling approach termed the “Movable Type” (MT) method, and a statistical energy function for solvation modeling... are developed and utilized to create an implicit solvation model...
June 02, 2014
There is a large body of evidence that many protein–ligand cocrystal structures contain poorly refined ligand geometries. These errors result in bound structures that have nonideal bond lengths and angles, are strained, contain improbable conformations, and have bad protein–ligand contacts. Many of these problems can be greatly reduced with better refinement models.
May 01, 2014
Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s).... Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-scaling, semiempirical quantum mechanics (SE-QM) program DivCon with the PHENIX X-ray refinement engine.
April 03, 2014
The impact of QM and QM/MM based X-ray refinement on our understanding of protein:ligand function is discussed in detail with examples including interaction decomposition diagrams, scores, and other values. This information is particularly interesting to structure based drug discovery practitioners.
January 01, 2014