Network Biology (Dec 2023)
In Silico Protocol for structure and function prediction of proteins in biological systems
Abstract
Proteins carry out the majority of the biological processes of living cells. These macromolecules are almost involved in every cellular process: replication and transcription of DNA, and produce, process, and biosynthesize other proteins. They are controlling cell division, metabolism, and materials and information transportation into and out of the cell. The understanding how living cells work requires revealing the structure and function of proteins. Our protocol aim is to analyze protein(s) structure and its function in biological systems. There are 9 steps of the protocol by which the protein(s) is extensively analyzed structurally and functionally. These steps are bioinformatics tools and software: Retrieving sequence of protein(s), Sequence alignment, Phylogenetic tree construction, Protein(s) 3D Structure Prediction and Refinement, Protein(s) 3D structure validation and visualization, Protein(s) Domain Identification, Subcellular Localization of Protein(s) and Interactome Analysis. The protocol links between the structure and function of the protein(s) and a heuristic to predict protein(s) function.
