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=Help me make a page for Protein-Protein Interaction Prediction=
==To Do List==
*0) limit to 6->10k words,(30->50 KB) of readable prose.
*1) What are protein-protein interactions.
*2) Why it is useful to be able to predict them with a computer.
*3) The general principles involved.
*4) You should aim for no more than a dozen, preferably review articles.
*5) Smaller articles on individual computational methods (vote: 1y:1n ).
*6) add links to related Wikipedia pages.
::6a) learn and use common wiki formatting principles
*7) integrate with Wikipedia.
*'''Note''' To-do list here, other comments should be left on talk page.
=Draft article begins here=
===The prediction of an interaction or binding between proteins.===
(computational multi [[genome]] [[assay]]s are of primary interest)
Protein-Protein Interaction Prediction is often referred to with the acronym (PPIP)
'''Protein-protein interaction prediction''' is a branch of [[bioinformatics]] that seeks to use computational methods to predict complex [[protein-protein interaction]]s. Understanding the functional [[interaction]]s of proteins is an important research focus in [[biochemistry]], often referred to as [[proteomics]].
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Since it's completion genome sequencing has become more accurate, less expensive, and quicker.
There are now many sequenced genomes waiting for study. However, it has become clear that the data of the DNA sequence is not enough. The [[human genome]] encodes between 40,000 and 100,000 [[protein]]s (the [[proteome]]), and in order to make use of the [[DNA]] sequence, [[protein sequence]]s must be predicted and verified, [[Protein structure]] predicted and verified, and [[Protein-protein_interaction]] predicted and verified.
Many methods exist to experimentally determine protein-protein interactions, including [[Affinity chromatography]], yeast [[two-hybrid screening]] techniques, [[fluorescence resonance energy transfer]] (FRET), and Surface Plasmon Resonance (SPR). However, with at least 40,000 unique protein sequences potentially available in every cell, the number of possible interactions becomes so enormous that physical testing can only be performed on a small subset of the most interesting proteins at grate expense. Protein-protein interaction prediction seeks to use advanced computational methods to rapidly investigate many possible interactions in order to identify those with the greatest potential for experimental investigation.
Knowledge is the first step Understanding the second and helping the third.
PPIP provides a means of gaining knowledge of how [[organism]]s work.
understanding how the inner workings of organisms makes it possible to develop a method of fixing organisms when broken and helping them resist attack
==Computational Methods==
Summary in general language, can refer to [[Protein structure prediction]], [[proteomics]], other concepts.
===Method 1===
Description can be somewhat more complext but not to the level of a technical journal
====Advantages and disadvantages====
===Method 2===
(if there are more than one important method)
====Advantages and disadvantages====
==Validation==
Predictions must be validated experimentally, however all experimental methods are costly and have numerous unavoidable associated error producing [[False_negative|FN]] and [[False_positive|FP]]. therefore choosing and understanding superior methods of verification is vary important
==Signifcant results==
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.
PPIP produces results that need biological verification and further exploration before the results can be used to cure diseases with new drugs or understanding.
The results are used heavily as a starting point for biological research where most of the metabolic pathway of interest is unknown.
Interperting the results of PPIP can be problematic because of the volumes of data generated therefore, the data is often organised in a hierarchical manner, or an [[interactome]]. The two best approaches are to simply display only one or two interaction links deep of a hierarchy at a time, the second is to assign the highly interactive (hub) proteins to be the roots of the interaction trees, creating groupings of functionally and spatially related proteins.
The main goal of [[proteomics]] is to predict the structures, interactions and functions of the proteins. Specific function is only found through interactions. The prediction of protein-protein interactions is of vital interest in proteomics.
==References==
==See also==
*[[Support_vector_machine]]
*[[Parallel_computation]]
*[[Proteomics]]
**[[Molecular_docking]]
**[[Protein_interactions]]
***[[Protein-protein_docking]]
*[[Structural_Bioinformatics]]
**[[Protein_structure]]
***[[Structural_domain]]
**[[Protein_folding]]
**[[Threading_%28protein_sequence%29]]
*[[Computational_genomics]]
*[[Biological_database]]
==External links==
*Online protein-protein interaction prediction services
**[http://advice.i2r.a-star.edu.sg/search/pair.php advice]
**[http://www-appn.comp.nus.edu.sg/~bioinfo/bayesprot/bayesprot.htm Bayesian Protein Prediction]
**[http://interdom.lit.org.sg/validate/index_inter.php InterDom]
**[http://www.russell.embl-heidelberg.de/people/patrick/interprets/interprets.html InterPreTS]
**[http://interweaver.i2r.a-star.edu.sg/report/demo.php InterWeaver]
**[http://cbi.labri.fr/outils/ippred/ Ippred]
**[http://ophid.utoronto.ca/ophid/ppi.html OPHID]
**[http://gordion.hpc.eng.ku.edu.tr/prism/predictions.php#online PRISM]
**[http://mysql5.mbi.ucla.edu/cgi-bin/functionator/pronav Prolinks]
**[http://www.protsuggest.org/main.html Protsuggest]
**[http://point.bioinformatics.tw/ POINT]
**[http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi SVMProt]
**[http://string.embl.de/ String]
*[http://www.ncbi.nlm.nih.gov/ PubMed]
*[http://www.kernel-machines.org/software.html kernel machines]
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