All Publications

in year '2013'

October 28, 2013
Accurately computing the free energy for biological processes like protein folding or protein−ligand association remains a challenging problem. Both describing the complex intermolecular forces involved and sampling the requisite configuration space make understanding these processes innately difficult. Herein, we address the sampling problem using a novel methodology we term “movable type” (MT)....
April 06, 2013
We describe a novel knowledge-based protein−ligand scoring function that employs a new definition for the reference state, allowing us to relate a statistical potential to a Lennard-Jones (LJ) potential. In this way, the LJ potential parameters were generated from protein−ligand complex structural data contained in the Protein Databank (PDB)....
March 27, 2013
We have provided a demonstration of how to use QM-based X-ray refinement to inform the often difficult choice about where to put a proton. This seemingly simple atom has given practioners in the field a lot of grief over the years, and it turns out that QM-based methods do a really good job of helping you make this important decision!
February 13, 2013
The recognition and association of donepezil with acetylcholinesterase (AChE) has been extensively studied in the past several decades because of the former’s use as a palliative treatment for mild Alzheimer disease. Herein, we examine the conformational properties of donepezil and we re-examine the donepezil-AChE crystal structure using combined quantum mechanical/molecular mechanical (QM/MM) X-ray refinement tools.....