All Publications

in year '2016'

October 15, 2016
The plasticity of active sites plays a significant role in drug recognition and binding, but the accurate incorporation of ‘receptor flexibility’ remains a significant computational challenge.... Herein, we describe the Movable Type with flexibility (MTflex) method that generates ensembles on the more relevant free energy surface in a computationally tractable manner.
October 03, 2016
We review our performance in the SAMPL5 challenge for predicting host–guest binding affinities using the movable type (MT) method. The challenge included three hosts, acyclic Cucurbit[2]uril and two octa-acids with and without methylation at the entrance to their binding cavities. Each host was associated with 6–10 guest molecules...
April 01, 2016
Gaining an understanding of the protein:ligand complex structure along with the proper protonation and explicit solvent effects can be important in obtaining meaningful results in structure-guided drug discovery and structure-based drug discovery. In the present work, we describe a novel scoring method, called XModeScore, which enumerates the possible protomeric/tautomeric modes, refines each mode against X-ray diffraction data with quantum mechanics and scores each mode using a combination of energetic strain (or ligand strain) and rigorous statistical analysis of the difference electron density distribution.