Saturday, May 16, 2009


About computational Biochemistry

Relevant Biotool lists common Biotools and site employed by a computational Biochemist

Reviews of the essentials of computational Biochemistry; importance and implication.

Understanding the use and the interpretations of the result of some Bioinformatic sites

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About Computational Biochemistry

Computational Biochemistry is not limited to just DNA and protein sequences as widely thought; it covers more than that. It encompasses the various computational tools (software and online Applications) that is used to aid the study of biochemistry. The recent advancement in the computing world had facilitated the availability of a vast array of tools to the modem biochemist. Computational Biochemistry itself is a subset of a broader subject, the Bioinformatic whose area of coverage is not limited to only Biochemistry, but also include other Bioscientific field.


The importance of the knowledge of computational biochemistry to a modern biochemist can be likened to the importance of computer to the literate community. Virtually every aspect of Biochemistry has been touched and influenced by computation.

In recent times computing has found immense application in different fields including Biochemistry. The application of computation to solving biochemical problems is becoming widespread. These include the acquisition of scientific literatures, analysis of protein and DNA sequence, and structures, understanding protein-protein and protein-carbohydrate interaction and functions, analysis of graphical results, statistical analysis of data.

Understanding computational Biochemistry enables a biochemist to easily acquire important information and other online resource for both educational and research purpose.

Available tools and resources

Currently, there are lots of free resource available online to an enlightened biochemist, the knowledge of computational Biochemistry would enable a biochemist to effectively annex these resource to achieve set goals. Such free resources include Biomedical libraries, protein and DNA sequences databank, interactive metabolic pathway tools, protein-protein interaction tools. see more listings of these free resources at the free online Biotool list

Feature and characteristics of Bioinformatic sites

A common feature of the online tools and resources of Bioinformatic site is their extensive cross-referencing. Most of these sites contain links to other online resource that offers more relevant information on the current query. In addition many informational sites has special numbers that they use to represent each entry indexed in their databases. This number is often referred to as accession number or ID. While some site prefer to use a more standardized identity system such as the EC number of an enzyme or the gene name, others prefer to use their own unique identity system. These IDs is what is used in cross-referencing the different bioinformatic sites together.

How to use Bioinformatic sites

The use of Bioinformatic sites depends on the nature of its operation for informational databases, a search is conducted in the text box provided with a generally accepted name of the query one then has to scan through the list of output result to pinpoint a specific search term. It is important to note the ID that the site used to represent the search query. This ID would be used for subsequent search. Using the ID to search for any term specifically opens up the desired entry.

Using Bioinformatic sites that offers online application usually require that the user understands the syntax and operation of the site before he or she can use them effectively. These sites, instead of containing Accession numbers or ID may contain “result ID” example of such site includes BLAST, CLAWSTAL, domain finders

Problems and limitation

There might be some limitation to the accessibility and use of this Bioinformatic resources, the primary fact is that since new online applications and tools are springing up daily, it is practically impossible to be conversant with the use of all these sites. A more realistic approach is the mastery of those sites and application that provides the set of information and services you want. Being aware of the existence and capability of a broader array of sites can be very helpful.

The other less serious limitation is the fact that one has to be “online” to be able to access these resources except if one opts to purchase the software that contains the same function and information of a site of interest.


As discussed earlier, the list of free Biotools available to a researcher is growing on a daily basis. We are now becoming more aware of how ICT could affect the advancement of Biosciences. Not only has bioinformatics facilitated the ease with which Bioscientific information is obtained, it also has a network of “like-sites” where similar information or more information could be obtained from a particular search term.

In all, computational Biochemistry is still an emerging and rapidly growing field that would be the bedrock of all biochemical studies in the nearest future. Avail yourself the opportunity to be “Bioinformatic literate”.

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