Predicting Protein Function using Decision Tree

The drug discovery process starts with protein identification because proteins are responsible for many functions required for maintenance of life. Protein identification further needs determination of protein function. Proposed method develops a classifier for human protein function prediction. The model uses decision tree for classification process. The protein function is predicted on the basis of matched sequence derived features per each protein function. The research work includes the development of a tool which determines sequence derived features by analyzing different parameters. The other sequence derived features are determined using various web based tools. Keywords—Sequence Derived Features, decision tree. I. PROTEINS AND THEIR ROLE ROTEINS are the primary components of living things, and they play many roles. Proteins are the molecular machinery that regulates and executes nearly every biological function [4]. Proteins provide structural support and the infrastructure that holds a creature together; they are enzymes that make the chemical reactions necessary for life possible; they are the switches that control whether genes are turned on or off; they are the sensors that see and taste and smell, and the effectors that make muscles move; they are the detectors that distinguish self from oneself and create an immune response. Proteins have a variety of roles that they must fulfill: • They are the enzymes that rearrange chemical bonds. • They carry signals to and from the outside of the cell, and within the cell. • They transport small molecules. • They form many of the cellular structures. • They regulate cell processes, turning them on and off and controlling their rates. Despite their radical differences in function, all proteins are made of the same basic constituents: the amino acids. Each amino acid shares a basic structure, consisting of a central carbon atom (C), an amino group (NH3) at one end, a carboxyl group (COOH) at the other, and a variable side chain (R), as shown in Fig. 1. Chains of amino acids are assembled by a reaction that Manpreet Singh is with the Department of CSE & IT, Guru Nanak Dev Engineering College, Ludhiana (e-mail: [email protected]). Parminder Kaur Wadhwa is with the Department of CSE & IT, Guru Nanak Dev Engineering College, Ludhiana (e-mail: [email protected]). Surinder Kaur is with Department of CSE, Institute of Engineering and Technology, Bhaddhal, Ropar (e-mail: [email protected]). occurs between the nitrogen atom at the amino end of one amino acid and the carbon atom at the carboxyl end of another, bonding the two amino acids and releasing a molecule of water. The linkage is called a peptide bond, and long chains of amino acids can be strung together into polymers, called polypeptides, in this manner. All proteins are polypeptides. When a peptide bond is formed, the amino acid is changed (losing two hydrogen atoms and an oxygen atom), so the portion of the original molecule integrated into the polypeptide is often called a residue. The sequence of amino acid residues that make up a protein is called the protein's primary structure. Fig. 1 Basic Chemical Structure of Amino Acid II. PROTEIN FUNCTION The definition of biological function is ambiguous, and the exact meaning of the term varies based on the context in which it is used. It is obvious that the biological function of a protein has more than one aspect. Take for example a protein kinase; in the biochemical aspect, a kinase’s function would be the phosphorylation of a hydroxyl group of a specific substrate. The scope of interest implied by this definition does not require any more than a ‘disembodied’ protein performing alone in vitro. However, proteins perform their function within an organism, and this has consequences ranging from the subcellular to the whole-organism level. In a physiological aspect, the same kinase may be part of a signaling pathway, where a protein both phosphorylates, and is phosphorylated by, interacting partners. A mutation in this kinase might cause a disease, so yet another aspect is a phenotypic or medical one. Therefore, when speaking of a protein’s function, we must always specify the aspect or aspects of the functional description [2]. Manpreet Singh, Parminder Kaur Wadhwa, and Surinder Kaur Predicting Protein Function using Decision Tree P World Academy of Science, Engineering and Technology 39 2008