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Bioinformatics approach for Secondary Structure Identification in beta-barrel fold proteins

Syamala Devi1 and Kalyani2
1. Department of Computer Science and Applications, Panjab University, Chandigarh
2. Indira Gandhi National Open University, New Delhi
*Corresponding author

There is a need for knowing the structure of proteins for various reasons in biomedical applications. However, the rate at which the structures of proteins determined is not at par with the sequences of proteins derived. Therefore, theoretical methods using knowledge based techniques became popular to predict structures. Bioinformatics techniques are used for sequence alignment and comparison in the past and several algorithms were used in doing so. Structure based sequence information will be useful in making a link between the structure and sequence. In the present paper attempts were made to make a database of sequences of known secondary structure elements of a popular protein fold, beta-barrel or TIM-barrel. A string of sequence would be screened against the database strings to find out the secondary structural score of the input sequence. Provision has been made to give the input and obtain the output through a web interface.

Key words:-Bioinformatics, protein structure, secondary structure, structure prediction, Needleman-Wunsch algorithm, TIM-barrel fold.

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