[phenixbb] HB_score in Ligand Identification

Li-Wei Hung lwhung at lbl.gov
Thu Aug 23 12:47:20 PDT 2012

Hi Brad,

The HB_score detects hydrogen bonds and inter-atomic clashes between 
ligand and protein.  This additional term usually helps differentiate 
best one among a few good fits.

If you use the default library, since it consists of a diverse set of 
candidate ligands, the outcome of fitting the same density could be very 
different. It is not unusual to see wide spread HB_scores.  In the final 
ranking, we use normalized HB_scores as one of the criteria.

Hope this helps.  I'll add these information to PHENIX documentation.  
Please feel free to ask me additional question related to 
ligand_identification on/off Phenix list.

Li-Wei Hung

Brad C. Bennett wrote:
> Hello to all-
> Where can I find a description of what "HB_score" is and how it is calculated in the Ligand Identification program in Phenix? I'm assuming this is a metric for hydrogen bonding capability/propensity of a fit ligand based on distance and angle to model atoms. I have an output rank list of the top 20 ligand fits, ranked by Z-score. The HB_score is all over the place: low = -0.59, high = 77.96, most are between 0-10. I think I understand the correlation coefficient and Z-score but how does the HB_score fit in with these?
> I can't find this in the documentation or in the Terwilliger et al. (2007) Acta D reference. Somehow I've "lost" the log file, so maybe the information is in there.
> Thanks in advance!
> Brad C. Bennett
> Research Associate- Mark Yeager Lab
> University of Virginia
> Molecular Physiology and Biological Physics
> 320 Snyder Building
> 480 Ray C. Hunt Drive
> Charlottesville, VA 22908
> Email: bcb3b at virginia.edu
> Lab phone: 434-243-2520
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