Changes: Hydrogen Bond Networks

Revision as of 13:29, 14 June 2015

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 Filter

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

Read the introductory blog

CPK coloring

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

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.

@@ Line 12: / Line 12: @@
 bkoep's clarification from the blog comments:
-<p>In Foldit, all CPK modes (including Score/Hydro+CPK) color <font color="#0000FF">nitrogen</font> atoms blue and <font color="#FF0000">oxygen</font> atoms red. Imagining blue donors and red acceptors is a helpful simplification, but is not strictly correct. While <font color="#0000FF">nitrogen</font> is <i>usually</i> a donor and <font color="#FF0000">oxygen</font> is <i>usually</i> an acceptor, there are exceptions to this rule. For example, "http://www.cryst.bbk.ac.uk/PPS2/course/section7/os_hres.gif shows that one <font color="#0000FF">N</font> of histidine can accept an H-bond, whereas the <font color="#FF0000">O</font> of serine can also donate an H-bond.</p>
+<p>In Foldit, all CPK modes (including Score/Hydro+CPK) color <font color="#0000FF">nitrogen</font> atoms blue and <font color="#FF0000">oxygen</font> atoms red. Imagining blue donors and red acceptors is a helpful simplification, but is not strictly correct. While <font color="#0000FF">nitrogen</font> is <i>usually</i> a donor and <font color="#FF0000">oxygen</font> is <i>usually</i> an acceptor, there are exceptions to this rule. For example, [http://www.cryst.bbk.ac.uk/PPS2/course/section7/os_hres.gif this] picture shows that one <font color="#0000FF">N</font> of histidine can accept an H-bond, whereas the <font color="#FF0000">O</font> of serine can also donate an H-bond. <span style="color:rgb(51,51,51);font-family:helvetica,sans-serif;font-size:12px;line-height:normal;">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!</span></p>
-http://www.cryst.bbk.ac.uk/PPS2/course/section7/os_hres.gif
-<span style="color:rgb(51,51,51);font-family:helvetica,sans-serif;font-size:12px;line-height:normal;">This link 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!</span>
 == Advice ==
+BitSpawnIRC:
-:52 BitSpawnIRC the key is not only to do network, but taking care of the quality of network, this means several things:
+:The key is not only to do network, but taking care of the quality of network, this means several things:
-:52 BitSpawnIRC 1.- maintaining a balance between basic and acid polar aminos
+:* maintaining a balance between basic and acid polar aminos
+:* Red links are so important as blue ones
-:52 BitSpawnIRC 2.- Red links are so important as blue ones
-:52 BitSpawnIRC 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
-:53 BitSpawnIRC If the quality is too low, break it until to do sure the polarity is balanced
-:53 BitSpawnIRC an example:
-:53 BitSpawn [http://fold.it/portal/files/chatimg/irc_190318_1433847204.png Image]
-:53 BitSpawnIRC this net is ok on all its links, but polars=68%, netscore=685: it is too basic
+: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.
-:53	BitSpawnIRC if I break a basic bond then
+:An example:
-:54 BitSpawn [http://fold.it/portal/files/chatimg/irc_190318_1433847236.png Image]
+::[http://fold.it/portal/files/chatimg/irc_190318_1433847204.png Image 1]: this net is ok on all its links, but polars=68%, netscore=685: it is too basic.
-:54 BitSpawnIRC 76%, netscore=766
+::If I break a basic bond then: [http://fold.it/portal/files/chatimg/irc_190318_1433847236.png Image 2] - 76%, netscore=766.
-:55 Wilm All done by hand?
-:55 BitSpawnIRC not all, but the balance in each net by hand
+:Not all done by hand, but the balance in each net by hand.