American Journal of Computing Research Repository, 2014, Vol. 2, No. 2, 38-43 Available online at http://pubs.sciepub.com/ajcrr/2/2/3 © Science and Education Publishing DOI:10.12691/ajcrr-2-2-3 Determination of Characteristic Frequency for identification of Hot spots in Proteins using Computational Simulations: a Review Sidhartha Sankar Sahoo * , Malaya Kumar Hota Department of Electronics and Telecommunication Engineering, Synergy Institute of Engineering & Technology, Dhenkanal 759001, Odisha, India * Corresponding author: sidhartha.nmiet@gmail.com Received July 08, 2014; Revised July 16, 2014; Accepted July 20, 2014 Abstract Proteins perform their functions by interaction with other molecules known as target. Protein-target interactions are very specific in nature and occur at predefined locations in proteins known as hotspots. For successful protein-target interaction both protein and target must share common spectral component known as characteristic frequency. Characteristic frequency is very importance since it forms basis for protein-target interactions, thus far various computational simulations have been used for determination of characteristics frequency. In this paper we have applied all computational simulations used till now and also use comparative study based on computational time and Signal to Noise Ratio parameter to stress the best suitable technique. All computational simulation works in this paper are done using MATLAB. Keywords: proteins, amino acids, Electron Ion Interaction Potential (EIIP), consensus spectrum, resonant recognition model (RRM), characteristic frequency, Discrete Fourier Transform (DFT), Chirp Z-Transform (CZT), Discrete Cosine Transform (DCT) Cite This Article: Sidhartha Sankar Sahoo, and Malaya Kumar Hota, “Determination of Characteristic Frequency for identification of Hot spots in Proteins using Computational Simulations: a Review.” American Journal of Computing Research Repository, vol. 2, no. 2 (2014): 38-43. doi: 10.12691/ajcrr-2-2-3. 1. Introduction Proteins are the probably the most important carrier and work force of every living organism. Proteins form the basis for major structural component of animal & human tissue. Proteins are the building blocks of life and are essential for growth of cells and tissue repair. Protein is natural polymer molecule consisting of amino acid unit. All proteins are made up of different combination of 20 compound called amino acids. Depending upon which amino acid link together proteins molecules form enzymes, hormones, muscles, organs and many tissues in the body [1]. Proteins are polymers of amino acid joined together by peptide bond. There are 20 different amino acids that make up essentially all the proteins on earth. An amino acid consists of a carboxylic acid group, an amino group and a variable side chain all attached to central carbon atom. The side chain is the only component that varies from one amino acid to another. Thus the characteristic that distinguish one amino acid from another is its unique side chain that dictates an amino acid chemical property [1]. Even though proteins can be imagined to be linear chain of amino acid, they are not present as linear chains in reality. They fold into complex three dimensional (3-D) structures and it is this folding ability that enables them to perform extreme specific functions. The information necessary to specify the three dimensional (3-D) shape of proteins is contained in its amino acid sequence. The 3-D structure of proteins is most stable form which a protein can attain and this 3-D structure is due to certain specialized regions in proteins known as hot spots [2]. Proteins perform their biological function by interacting with other molecules known as targets and the necessary binding energy for this protein-target interaction is provided by hot spots. Hot spots are small groups of amino acids which provide functional stability to proteins, so that protein can efficiently bind with a target and thus can perform its biological function. The hot spots in proteins can be identified by the use of Resonant Recognition Model (RRM) [3], which correlates the biological functioning of the protein to the characteristic frequencies. These hot spots in proteins can be localized where the characteristic frequencies of the functional groups are dominant. The computational simulations [4] can be used to extract these characteristic frequencies in the protein sequences which are primarily based on the sequence information only. Previous successful attempts have been made for determination of characteristics frequency using Discrete Fourier Transform (DFT) [5-9], Chirp Z-Transform (CZT) [10] and Discrete Cosine Transform (DCT) [11-12] which are discussed in this paper. The rest of the paper is organized as follows. Section 2 gives brief definition of