[phenixbb] QuantumBio Release: XModeScore & DivCon Discovery Suite v7.1

Lance Westerhoff lance at quantumbioinc.com
Mon Jan 16 19:58:11 PST 2017

Hello All-

I trust everyone had a nice holiday break and a Happy New Year!

Today, we are excited to kick the new year off with a new release of our QM/MM refinement and analysis plugin for the Phenix platform. The full announcement, along with links to the details and licensing information, is available at this URL:


Thanks to our many users - academic, industrial, and government - who have provided feedback and support for this effort. This plugin, available within the DivCon Discovery Suite version 7.1, has a number of significant improvements applicable to users of Phenix including:

 * QM/MM X-ray Refinement Standard: Version 7.1 represents a complete overhaul of our MM and QM/MM implementation for improved stability, performance, and usability. Our fully automated QM/MM implementation has now come out of "beta" status and it is ready for production use. The implementation also supports truncated residues, multiple regions, and integrated ligand atom typing.

 * Application: Fragment Based Drug Design: Phenix/DivCon coupled with the novel, our patent pending XModeScore tool has been applied to several key areas including protomer/tautomer determination, binding mode selection, crystal water positioning, and now even fragment-based screening. We have provided a tutorial of MOE-based fragment docking coupled with XModeScore-based selection.

 * New Structure/Chemistry Analyses: The question we often hear from new users is how one can evaluate the performance of QM and QM/MM X-ray refinement vs. more conventional methods. We have now packaged several before/after analyses within refinement including Clash Scores (using phenix.molprobity); Strain, Interaction Energies, and ZDD (using DivCon); and GBVI/WSA dG binding score prediction (using MOE - as available).

 * New Feature [beta] - Protonation: Fast, integrated protonation and hydrogen bond network optimization is a perpetual problem in the field (especially in X-ray crystallography). This method uses a combination of dead end elimination and graph theory along with crystallographic symmetry and density - as available - to quickly and accurately determine the correct protonation states of bound ligands, active sites, waters, and protein/DNA/RNA.

If you are interested in using or evaluating our linear scaling, quantum mechanics software in your drug discovery efforts or if you would like to schedule an on-line or on-site meeting to discuss the technology, please email sales at quantumbioinc.com and let us know. And as with last year, we are waiving the license free for non-profit, academic users as per academic license agreement. Our academic, commercial, consulting, and evaluation licenses are available on-line (most for electronic signature):


Have a great 2017!

Lance M. Westerhoff, Ph.D.
President and General Manager
QuantumBio Inc. 

WWW:    http://www.quantumbioinc.com
Email:    lance at quantumbioinc.com

Phone:   814-235-6908
Fax:        814-235-6909

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