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Structural Bioinformatics

Definition
• Structural bioinformatics is the branch
of bioinformatics that is related to the analysis and

prediction of the three-dimensional structure of
biological macromolecules such as proteins, RNA,
and DNA

Objective
• The creation of new methods of analyzing and

manipulating biological macromolecular data in
order to solve problems in biology and generate
new knowledge
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Novel functions of a protein is more

explored from its structure , which cannot be observed
in sequences
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• Protein structures are classified into four

levels: primary (sequences), secondary (local conformation of the
polypeptide chain), tertiary (three-dimensional structure of the protein
fold), and quaternary (association of multiple polypeptide structures)
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Protein Structure Visualization
• Cartoon: this type of protein visualization highlights the secondary
structure differences
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• Lines: each amino acid residue is represented by thin lines, which
allows a low cost for graphic rendering
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• Sticks: each covalent bond between amino acid atoms is
represented as a stick
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Other structural databases
• MMDB : Experimentally determined three-dimensional structures of
biomolecules derived from Protein Data Bank (PDB)
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Why do compare protein structures ?
• Structures are more conserved in evolution
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• Structural similarity essential to determine the protein
function
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• Distances between aminoacids in the protein
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• Prediction of local structural regions is easier
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• Programs in the field often employ different types of machine
learning approaches
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• Statistically significant score tells the input
protein adopts similar 3Dstructure to that of
the common fold
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• If function is perfect, we will be able to scan all the
possible conformations by detecting the correct fold
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• Molecular docking aims to predict possible poses
(binding modes) of the ligand when it interacts with
specific regions, generally restricted by a box, in the
receptor
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