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Bioinformatics is an advanced field of molecular biology. Genomic projects provide thousands of genes and protein sequences to be deposited in the data bases in the web. This resulted in the development of software and bioinformatics tools to analyze the information present in these sequences with for phylogenetic origins, protein structure and function. In addition, application of bioinformatics in drug design as bio-medical and pharmacological sciences seeks for new targets and novel agents. This manual contains useful information about the software and online servers for analysis and prediction of primary, secondary and tertiary structure of protein. The predicted structure are used to elucidate protein function, interaction and active site which play an essential role in predicting binding affinities with ligands as preliminary step in drug design.