[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,
Tim
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
> X-Ray Laboratory Manager Tel. (+44) 020 7153 5445
> Section of Structural Biology Fax. (+44) 020 7153 5456
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