Talk:Protein-protein docking

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[edit] Field of what

If anyone can provide an example of Protein-protein docking being performed by a theoretical or quantum chemistry group, then that could be reinstated.. otherwise I think it is misleading. Zargulon 09:36, 5 September 2005 (UTC)

I am not an expert in this field but I cannot imagine how theoretical biochemistry could not be considered as a subfield of theoretical chemistry or quantum chemistry. I guess the people doing protein-protein docking are using density functional theory, molecular mechanics or molecular dynamics, aren't they? Are the methods used in protein-protein docking ignoring quantum mechanics? Theoretical chemistry is defined as any non experimental reasoning applied to chemistry not as what are doing theoretical (or quantal) chemistry groups. Quantum chemistry is defined by the application of quantum mechanics to chemistry whoever does this. Am I wrong? --09:57, 5 September 2005 (UTC)

Density functional theory is not used. Molecular dynamics is used only by a minority and with negligible success. Protein-protein dockers are happy with heuristic solutions which use, for instance, residue contacts, or shape complementarity of molecular surfaces. Theoretical chemistry approaches are generally too time consuming to be useful in the case of even a small protein. There is some limited cross-fertilization of ideas but they are different communities and address different questions. Zargulon 23:53, 5 September 2005 (UTC)

OK Thanks. I understand better. Do those heuristic solutions have something to do with molecular mechanics? I nevertheless think what they do is somehow theoretical chemistry. Because it is a non experimental reasoning.Vb13:51, 6 September 2005 (UTC)~

Yes, some heuristic methods occasionally use parameters from molecular mechanics force fields (like CHARMM or AMBER). It is a matter of finding something that works! Zargulon 18:06, 6 September 2005 (UTC)

OK I have re-edited to link with theoretical chemistry but not with quantum chemistry. I guess you now agree --131.220.68.177 08:56, 7 September 2005 (UTC)

I don't agree with the first sentence, but I agree that there should be a link to theoretical chemistry, which I am retaining. the point about CHARMM and AMBER is that protein-protein dockers hijack the parameter sets from these codes, not that they actually run them. Zargulon 10:01, 7 September 2005 (UTC)

Also I am removing the link to computational chemistry.. it sounds like it is a good idea, but it becomes clear from looking at the introduction to the computational chemistry page that there is absolutely no overlap with protein-protein docking at all! Zargulon 10:01, 7 September 2005 (UTC)

[edit] Merge

Disagree Zargulon 11:34, 6 January 2006 (UTC)

Disagree. I am against merging this article with the one on Protein-protein interactions. Protein-protein docking is a bioinformatics method. Protein-protein interactions are an observable.--Miguel Andrade 15:20, 24 January 2006 (UTC)

Thanks for the clarification. I've removed the merge tags. However, I am wondering why there is no wikilink or direct mention of protein-protein interactions, but only of interaction. --Uthbrian (talk) 18:28, 24 January 2006 (UTC)