[phenixbb] Estimation of ligand binding affinity by occupancy refinement

Timothy Springer springer at idi.harvard.edu
Tue May 1 06:50:14 PDT 2012

what does this have to do with estimating ligand binding affinity? Does one have to have fairly low occupancy? I have examples where one end of a ligand is much better defined than the other end of the ligand, both ends are in the same pocket. The pocket has to reshape to accomodate high affinity binding. We have modeled complete occupancy, but B factors for example would differ and we go from two conformations in rather diffuse density to excellent density at the one end of the pocket, while at the other end there is always excellent density. It seems magical to convert this type of data to affinity, but if there was a way, I would be interested in trying it.
With my best regards,

Timothy A. Springer, Ph.D.                                    
Latham Family Professor of Biological Chemistry and Molecular Pharmacology                                     
Harvard Medical School                   http://idi.harvard.edu/springer 
Immune Disease Institute                 springer at idi.harvard.edu        
Program in Cellular and Molecular Medicine, Dept. Medicine
Div. Hematology                                 Children's Hospital Boston
3 Blackfan Circle, Rm 3103              phone:  617-713-8200                
Boston MA 02115                               fax:        617-713-8232                

On May 1, 2012, at 9:32 AM, Nora Cronin wrote:

> I'm having a small problem with format - entering fixed_ensembles in automr:
> my input:
>  fixed_ensembles {
>    fixed_ensembleID_list = "ensemble_1"
>    fixed_euler_list = 87.09  64.28 257.24
>    fixed_frac_list = 0.540  0.079  0.069
>    fixed_frac_list_is_fractional = True
>  }
> Phenix output:
> Adding Ensemble  ensemble_1  as fixed solution with:
> Euler angles:  [87.09, 64.28, 257.24]
> Coords (orthogonal A):  [0.54, 0.079, 0.069]
> *************ERROR ENDING *******************
> ****************************************
> AutoMR Input failed
> Python argument types in
>    SOLU.addSOLU_6DIM_ENSE(InputMR_AUTO, str, list, bool, list, float, bool, bool, bool)
> did not match C++ signature:
>    addSOLU_6DIM_ENSE(phaser::SOLU {lvalue}, std::string, scitbx::vec3<double>, bool, scitbx::vec3<double>, double, bool, bool, bool, bool, scitbx::vec3<double>, double)
> ****************************************
> *************ERROR ENDING *******************
> [1
> In addition to fixed two solutions is it necessary to repeat the key phrases or can one add to "fixed_euler_list" in groups of three (do they need to be comma delimited?
> Nora
> Dr N B Cronin
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