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 assays 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 interactions. Understanding the functional interactions of proteins is an important research focus in biochemistry, often referred to as proteomics.
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 proteins (the proteome), and in order to make use of the DNA sequence, protein sequences 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 organisms 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 FN and 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.
References
See also
External links
- Online protein-protein interaction prediction services
- PubMed
- kernel machines