I am trying to design multi-target directed ligands. I have found some similar common ligands for both proteins. When I docked these ligands I have seen the score is almost similar. But these ligands are not that much potent compared to other inhibitors. So I wanted to modify them and achieve some good potency. So can anyone please tell me how to compare the active sites of two different proteins?
The following links describe methods that should be helpful. The first link is to Ligplot, which provides 2D visualizations of protein-ligand interactions when provided a 3D structure or model of the complex. This is a very good way to see the differences, at least on a "first pass". (Are you confident in your docked models?) CPASS (second link) will provide similarity measures and "scores" that are likley to differ from the score you obtain from your docking program. The remaining links are to articles on this topic.
http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/
http://cpass.unl.edu/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689763/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2804948/
http://members.cbio.mines-paristech.fr/~jvert/svn/bibli/local/Kellenberger2008How.pdf
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-99
http://bionmr.unl.edu/files/publications/55.pdf
Dear Keith. Thanks for the detailed description. I will see these links and will use it for my studies
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