Protein Function Prediction
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Contents
[edit]Introduction of protein function prediction
Recently, tons of protein sequence information has been available as a result of whole genome sequencing project of many organisms. However, it is almost impossible to reveal their potential functions by experimental methods only. Also, we are faced with a rapidly increasing number of proteins whose structures are known but whose functions are not. That is why currently people are giving attention to the computational approaches in which plenty of protein functions can be predicted simultaneously with reasonable accuracy. Furthermore, when we can deal with personal genomes in the future (a period of personal genomics), it is more important to predict diverse proteins resulted from individual's DNA sequence polymorphism. Therefore, computational protein function prediction methods can be a powerful tool for the biological research.
[edit]Function Annotation schemes
For protein function prediction, standard function annotation scheme is required.
There are two generally used function annotation schemes, EC and GO for these purposes.
[edit]Protein function prediction methods
Protein function prediction methods can be basically classified according to information sources.
1. Sequence-based approach is the most basic method. It utilizes BLAST, Sequence motif & domain information, and Important residue information.
2. Structure-based approach takes use of structural information. It Compares overall three-dimensional shape, or Locate functional local regions. Also, Prediction without structural alignment is possible.
3. Protein-protein interaction-based approach : There are diverse methods such as FunctionalFlow method, Global mapping of unknown proteins, Finding cliques in protein interaction networks, and Evidence integration in PPI networks.
In addition, there are other methods different from above.
4. Annotation frequency based approach
5. Total information combination approach
[edit]Web-servers
There are various Web-servers to predict protein function. Generally these web-servers predict protein function to given query protein sequence using their own novel methods.[edit]Databases
There are various Databases for protein function prediction.
[edit]Conferences
Information about related Conferences and meetings available. Currently, AFP(Automated Function Prediction) conference is mostly aiming at this issue.
[edit]Discussion
Discussion section. Let's talk about protein function prediction.[edit]See also
- Network biology wiki : This wiki site covers all the biological network concepts. Visiting this site could help understand the PPI(Protein-protein interaction)-based approach that is analyzed in this wiki more easily.
- CASP : Its goal is to help advance the methods of identifying protein structure from sequence. The Center has been organized to provide the means of objective testing of these methods via the process of blind prediction. In addition to support of the CASP meetings, our goal is to promote an evaluation of prediction methods on a continuing basis. CASP experiments aim at establishing the current state of the art in protein structure prediction, identifying what progress has been made, and highlighting where future effort may be most productively focused.
- BioCC
- KOBIC
