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1054: Vancomycin Binder: Shape Complementarity

Closed since about 11 years ago

Intermediate Overall Design

Summary

Created
February 13, 2015
Expires
Max points
100
Description

Design a binding pocket for vancomycin! Antibiotic resistance is an increasing problem and one of the last resorts for treating inflammation is the cyclic peptide vancomycin. Hence there is a general interest to generate proteins that can bind vancomycin and upon binding generate a signal. With this technology it would be possible to test patients that have been treated with antibiotics if they still have small amounts left before they leave e.g. a hospital. The aim of this puzzle is to optimize the interaction between a protein and the small molecule vancomycin.

This puzzle also introduces the new Shape Complementarity filter. Shape complementarity is a measure of how well the ligand's surface contours match the cavity of the binding pocket, and has been shown to be a good discriminator between binders and non-binders. Use the "Show Isosurface" view option to visualize the protein surface, and increase shape complementarity to improve your score!

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Comments

spmm Lv 1

mine's broken - Mac Yosemite - the black cloud goes if I turn the isosurface off and it didn't crash, moving the ligand about doesn't fix it.

mottiger Lv 1

I'm sure you are also interested in different orientations of the vancomycin and the corresponding folds?

Bruno Kestemont Lv 1

(Windows 7) The cloud appears or not when cliking on "Show Isosurface" depending on the solution I load. Even then , it sometimes arrounds also the ligan or not.
And I do not see any change when clicking on "show" for the new filter.

bkoep Staff Lv 1

Thanks for all the bug reports relating to the "Show Isosurface" option! We'll try to reproduce these on our end and see if we can figure out the problem.

bkoep Staff Lv 1

Clearly, we'd like players to focus on building a binding pocket on the concave side of the protein (where mutations are allowed).

But, by all means, experiment with different orientations of the ligand in the binding pocket to maximize packing and shape complementarity!

bkoep Staff Lv 1

In this puzzle, players can receive a maximum of 1500 points from the Shape Complementarity filter. But beware, there is a steep penalty if your shape complementarity drops too low, and the bonus will jump from 1250 to 250!