Talk:Protein–protein interaction prediction

message: *This article was originally marked for deletion however it was not found in violation of standards (WP:OR and WP:NOT and WP:NOR) and is considered a valuable Wikipedia topic. Please feel free to contribute to a cleanup of this article.--Tim 20:04, 11 March 2006 (UTC)
thread_title: cleanup

message: This article selects a few methods for inferring direct physical interaction between pairs of proteins. But for the most part it does not address inferences that link proteins to each other through biological process rather than direct physical interation (conserved operon structure, etc). It also misses Rosetta stones, one of several techniques from David Eisenberg and colleagues. I would have expected an article like this to talk more about the general issue of finding that two protein families are linked, citing all the major post-homology methods. This Wikipedia article may actually serve to lead readers away from good published reviews of this important topic, and therefore do some harm.
For a long time, this article gave the name "phylogenetic profiling" to what is actually a different technique - inference of physical interaction from similar phylogenetic trees, and I waded in here only to correct that fault. This article continues to need help. Daniel haft (talk) 05:12, 8 April 2008 (UTC)
thread_title: Focus of article differs from reasonable expectations

message: This is a pure logorrhea, the author obviously does not know what he is talking about, there are a lot of references at the end of the article but correspond to relevant part of the text. The vocabulary is inappropriate in most of the article as well.
Here is a non exhaustive list of errors and inaccuracies:
*Genetic code is used instead of sequencing of the Human genome
*There is no such a thing as protein sequences being predicted and verified, once the cDNA is sequenced the protein sequence is known, thanks the the Genetic code.
*Protein structures don't need to be predicted, although a very interesting and valid field of research, the vast majority of protein structures known have been solved by X-ray crystallography, NMR or Cryo-EM.
*Only a fraction of the different proteins in the genome is expressed in each type of cell, therefore a lot less than 40000 but I don't have references.
*"Knowledge is the first step Understanding the second and helping the third", that's mambo jambo!
*"PPIP provides a means of gaining knowledge of how organisms work", even worse and very simplistic, organisms can't be summarised by their protein interactions.
*I looked in PubMed for the interaction between BUB3 and ZNF207, found nothing, the only thing I found was the BUB3 is a mitotic checkpoint protein and ZNF207 a zinc finger transcription factor thus likely to give a lot of noise in yeast two-hybrid screening experiments (this is my prediction, I'm not a specialist, anyone who knows about it is welcome to contribute).
*Don't quite understand the Dynamics method, what are the rules the author is talking about? if it is the rules of ab-initio folding using quantum mechanics, for the moment it only works on small peptides so it's just fantasy.
*The most effective Folding Prediction Method predicts, no comment, the style says all.
*Folding and Docking, why trying to work with proteins with no known structure when there are already 35579 structures in the PDB waiting for docking experiments. If you want to do this on a genome wide scale, a lot of the interactions can already be ruled out from functional anotation and subcellular localisation or cell type, that would reduce the search space, but given that multi-protein interactions would have to be considered the problem is exponential from a computing point of vue.
*Validation, "Predictions must be validated experimentally", what is the point to make some predictions if you need to validate them experimentally after? If your predictions are reliable there's no need, if they are not reliable they have no use.
*Significant results, the author speaks like the method was widely used with lots of results without giving a single verifiable example. 
*"many new drugs and biological understandings are developed starting with PPIP before moving on to experimental methods, saving time and millions of dollars in the process.", sorry but the only type of machine that could scratch the surface of the problem is something like Blue gene with an army of bioinformaticians and it is not cheap!
*References, most of the references are not relevant to the article, and the article does not mentions the references as it should do, in addition, in the Advantages and Disadvantages of Folding and docking, there is a [52], that looks like a cut and paste from a book or a scientific paper, actually a much neede reference which is probably missing in the list of references at the end of the article. Not to mention the evil problem of copyright infringement.
Blastwizard 02:22, 18 March 2006 (UTC)
thread_title: Very bad article too much to clean

message: I removed a few specific threshold values (eg, r>0.8 for phylogenetic distance matrix correlation) because, while these were presumably the values used in the paper that described the method, as far as I know the cutoffs themselves are fairly arbitrary. Not everyone who uses these methods will use the same cutoffs. Opabinia regalis 06:50, 15 May 2006 (UTC)
thread_title:  specific threshold values 

message: What is the wikipedia policy regarding those links? Some are commercial sites, others are just directory listings. Anybody know? --Rajah 17:28, 4 July 2006 (UTC)
replies: text: I removed the commercial link as it was irrelevant to the topic anyway. Blastwizard 06:28, 5 July 2006 (UTC)
thread_title: Servers links