Computational Tools for Structural Analysis of Proteins

Experimental approaches for identifying protein structures and conducting their analyses face systemic limitations and challenges. Thus, computational approaches have emerged as invaluable tools over the past few decades, offering complementary insights into the protein structure, function and analysis. This chapter provides a focused overview of computational tools being developed for predicting and analyzing protein structures. Acquisition and validation of protein structures is initially discussed, focusing on prominent resources such as the Protein Data Bank (PDB) and the AlphaFold Protein Structure Database. This section is followed by an overview of tools to study protein interactions, characterization of functional sites and visualization of protein static/dynamic state. Finally, we conclude with a meticulous discussion of the unaddressed challenges and future directions.