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Hydrogen Bond Networks

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A Hydrogen Bond Network is a 'web' of hydrogen bonds that connects the sidechains of multiple residues. When constructed across protein interfaces, these networks help to make the interface more stable.

Hydrogen Bond Network FilterEdit

Introduced in May 2015 this filter allows folders to improve the stability of their folds.

Read the introductory blog

CPK coloringEdit

bkoep's clarification from the blog comments:

In Foldit, all CPK modes (including Score/Hydro+CPK) color nitrogen atoms blue and oxygen atoms red. Imagining blue donors and red acceptors is a helpful simplification, but is not strictly correct. While nitrogen is usually a donor and oxygen is usually an acceptor, there are exceptions to this rule. For example, this picture shows that one N of histidine can accept an H-bond, whereas the O of serine can also donate an H-bond. This picture in particular should be helpful for determining how many hydrogen bonds are required to completely satisfy each residue type. For example, note that the N of tryptophan can only make one H-bond, whereas the N of lysine can make three!

Advice Edit

BitSpawnIRC:

The key is not only to do network, but taking care of the quality of network, this means several things:
  • maintaining a balance between basic and acid polar aminos
  • Red links are so important as blue ones
It gives much more score to have a red link that enhances the polarity of the entire network, that having a blue link that gets it worse. If the quality is too low, break it until to do sure the polarity is balanced.
An example:
Image 1: this net is ok on all its links, but polars=68%, netscore=685: it is too basic.
If I break a basic bond then: Image 2 - 76%, netscore=766.
Not all done by hand, but the balance in each net by hand.

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