Short peptides represent an important class of small molecules, abundant in nature, and they are involved in various biological activities. The short peptides are present in almost all living organisms, from single-cell bacteria to multicellular plants and animals. Peptides are essential components of the innate immune system and defend against invading pathogens. Hence, bioactive peptides have great research potential in biological and biomedical fields, especially in the pharmaceutical industry, peptides constitute a promising choice for developing less toxic, safer conventional drugs. The peptides are being used to treat microbial infections, slow down the aging process, reduce inflammation, develop nutraceuticals, etc. Due to the improved biocompatibility, research potential, and increased application opportunities, efforts are dedicated to peptide synthesis. The improvement in sequencing technologies has helped in the discovery of novel natural peptides, and manipulate peptide biosynthetic pathways. Bioactive peptide discovery, synthesis, biochemical feature prediction, protein-peptide interaction, docking, and molecular simulation studies require sophisticated computational tools. Hence, this review intends to present the key recent developments in this rapidly expanding field of bioinformatics exclusively for peptide research.