Published Research

Our scientists and customers actively collaborate on a wide range of basic theoretical discussions of QuantumBio's proprietary technology to more application-oriented discussions of the software's capabilities. Please see the list below for the most current publications highlighting QuantumBio's product line.

 

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.
November 10, 2015
In this article, we extend the movable type (MT) sampling method to molecular conformational searches (MT-CS) on the free energy surface of the molecule in question. Differing from traditional systematic and stochastic searching algorithms, this method uses Boltzmann energy information to facilitate the selection of the best conformations....
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...

 

 

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