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What is structural bioinformatics?
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What is structural bioinformatics?
This is the branch of bioinformatics that deals with the analysis and prediction of the 3D structure of proteins, RNA and DNA. Similarly to structural biology, its computer science counterpart aims at creating new methods to process data about macromolecules in order to solve concrete problems, for example in medicine and pharmacology.
To grasp the practical sense of structural bioinformatics it is appropriate to focus on the difference between “sequence” and “structure”. A surprising aspect is given by the total perceptive distance between the sequence of a genome and the actual shape of the protein, comparable to the 3D model of its molecular structure. Seemingly similar amino acid sequences can turn out to be protein structures that look absolutely nothing alike, since their folding expresses very different three-dimensional shapes.
The calculation of protein folding is one of the areas of study in which bioinformatics has provided a fundamental contribution, moving from laboratory techniques to simulations based on distributed computing, such as the collaborative projects Rosetta@Home and Folding@Home, which employ the unused resources of computers to support complex simulations of protein structures.
Another open source initiative to support protein folding is characterized by Foldit, a real game in which each user can use his or her ability to fold three-dimensional structures and share them with the project’s global platform.
If the three cases mentioned above were or are accessible to everyone, there are at the same time some initiatives reserved to research groups, such as the famous CASP (Critical Assessment of protein Structure Prediction), which has been held on a biennial basis since 1994.
University and private teams (supported by multinational AI companies) compete to identify computational methods capable of predicting the 3D structures of proteins as accurately as possible. The goal of CASP is to find solutions that are more efficient, faster, and cheaper than laboratory technologies such as X-ray crystallography or NMR spectroscopy.
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