In protParam, the molecular weight of protein is calculated by the addition of average isotopic masses of amino acids in the provided protein and the average isotopic mass of one water molecule. The various parameters computed by ProtParam are molecular weight, amino acid composition, extinction coefficient, estimated half-life, theoretical pI, and grand average of hydropathicity (GRAVY), aliphatic index and instability index. The protein can either be specified as a UniProtKB/Swiss-Prot or UniProtKB/TrEMBL accession number or ID or as sequences of amino acids. The protein sequence is the only input provided to calculate such parameters. It is used for calculating various physiochemical parameters of a provided protein.
ProtParam is one among the protein analysis tool available on the ExPasy server and can be accessible through the link.
It provides access to several scientific databases and software tools in many areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc.
ExPASy is the SIB Bioinformatics Resource Portal. There are different tools available through ExPasy server to analyze a protein sequence. The quaternary structure is formed by several protein molecules or polypeptide chains.Ī pictorial representation of primary, secondary, tertiary and quaternary structure is shown in figure 1.įigure 1: Representation of primary, secondary, tertiary and quaternary structure of proteins The three dimensional structure of a single protein molecule refers to the tertiary structure. Alpha helices and beta sheets are the two important secondary structures in protein. The intermolecular and intra-molecular hydrogen bonding between the amide groups in primary structure of protein form secondary structure. The linear sequence the polypeptide chain of amino acid refers to the primary structure of proteins. The protein structure is classified into primary, secondary, tertiary, and quaternary. The structure explains the different levels of organization of a protein molecule. Proteins differ from one another in their structure, primarily in their sequence of amino acids. A peptide bond is formed when the carboxyl group of one amino acid is linked to the amino group of another molecule through a covalent bond. In proteins, the amino acids are linked to each other by means of peptide bonds. There are almost 20 amino acids found in human body that usually varies in their R groups. The building blocks of proteins are amino acids. Amino acids are made from an amine (-NH2) and a carboxylic acid (-COOH) functional groups as well as a side chain which is specific to each amino acid. Some of the important functions such as DNA replication, catalysis of metabolic reactions, transportation of molecules from one location to another etc. Proteins have a wide range of functions within all the living beings. Proteins are one of the important fundamental units of all living cells. To introduce a protein analysis software that is available through the ExPASy server.To perform primary structure analysis of proteins.To compute the various physical and chemical parameters of a protein.