Molecular Docking

NAP peptide and Risperidone binding prediction to EB3

Molecular docking is the computer- aided prediction of a binding mode of two macromolecules or a small molecule to 

In the prediction process we take into consideration geometrical match, as well as evolutionary conservation of the binding pocket or interface, as well as electrostatic and hydrophobic match. 

We predict the binding mode of small molecules (such as drugs) to a protein with known 3D structure. It is possible to calculate binding affinity.

We predict the preffered binding mode of two (or more) proteins, or protein-DNA complex.

It is important to note that docking methods assume binding.
They are not designed to asnwer the question "Will these two proteins bind each other?" However, it is possible to compare binding affinity of various complexes.

 

Examples:

 

  • Risperidone and NAP protect cognition and normalize gene expression in a schizophrenia mouse model. Vaisburd S, Shemer Z, Yeheskel A, Giladi E, Gozes I. Sci Rep. 2015 Nov 10;5:16300. (Abstract) (Full Text)
  • D538G Mutation in Estrogen Receptor-α: A Novel Mechanism for Acquired Endocrine Resistance in Breast Cancer.. Merenbakh-Lamin K, Ben-Baruch N, Yeheskel A, Dvir A, Soussan-Gutman L, Jeselsohn R, Yelensky R, Brown M, Miller VA, Sarid D, Rizel S, Klein B, Rubinek T, Wolf I. Cancer Res. 2013 Dec 1;73(23):6856-64 (Abstract) (Full Text)

 

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