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Lecture2-Structural Bioinformatics

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14 views

Lecture2-Structural Bioinformatics

Uploaded by

shoyo3918
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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Structural Bioinformatics

Dr. Y. V. Lokeswari
Associate Professor
SSN College of Engineering
Structural Bioinformatics
• Structural Bioinformatics represents the subset that deals, directly or indirectly, with the structure of
macromolecules.
• Structural bioinformatics includes study of the structures of DNA, RNA, and proteins.

Conceptual organization of resources in structural bioinformatics


Structural Bioinformatics
• Primary Sources: The files containing atomic coordinates are uninformative to the
majority of structural biologists.
• Eg: Protein Data Bank (PDB)
• Algorithmic tools (applications) that transform, classify, analyze, and model this
primary data.
• Eg: CE (combinatorial extension, structural comparison of proteins)
• Secondary Sources: The results of the data analysis are often (but not always)
stored in other databases, they contain value-added information.
• Eg: structural alignments of proteins
• Algorithmic tools and the secondary resources can be divided into several broad
categories:
• Visualization,
• structural classification,
• structural alignment/structure modelling,
• structure prediction, and
• protein-protein/ protein-ligand interactions
Primary Resource
Protein Data Bank (PDB)
https://www.rcsb.org/
Protein Data Bank
• Protein Data Bank (PDB), at http//www.pdb.org, now https://www.rcsb.org/ the first biological
database, was established in 1971 to store 3D biological macromolecular structures.
• Originally housed at Brookhaven National Laboratories, USA, it is now managed and maintained by
the Research Collaboratory for Structural Bioinformatics (RCSB). https://www.rcsb.org/
• The PDB contains publicly available 3D structures of proteins, nucleic acids, and a variety of other
complex biomolecules experimentally determined by X-ray crystallography, (Nuclear Magnetic
Resonance Spectrometer) spectroscopy, and, most recently, cryoelectron microscopy.
• Data Format
• Consists of a collection of fixed format records that describe the
• atomic coordinates,
• chemical and biochemical features,
• experimental details of the structure determination, and
• some structural features such as hydrogen bonds and secondary structure assignments.
• dictionary-based format is the macromolecular crystallographic information file (mmCIF).
• The underlying data organization in an mmCIF is a set of relational tables.
• The mmCIF dictionary is an ontology that describes macromolecular structure and the various
experiments used to derive it.
Protein Data Bank
• Data Processing and Quality Control
• 3 steps: data deposition, validation and annotation.
• Validation refers to the procedure for assessing the quality of deposited atomic models
(structure validation) and for assessing how well these models fit the experimental results
(experimental validation).
• Annotation refers to the process of adding information to the entry.
• The PDB uses accepted community standards to validate structures.
• A number of checks are run and the results are summarized in an email directly
communicated to the depositor.
• Future of PDB.
• It uses Enterprise Java framework and is based on the MVC
(Model, View, Controller) design pattern.
Protein Data Bank
Visualization.
• Visualization is important to help users interpret scientific data in many areas of
bioinformatics.
• In structural bioinformatics, the foundation is the 3D structure of biological macromolecules,
which can only be interpreted using a molecular graphics program.
Protein Data Bank
• Protein Data Bank
• https://www.rcsb.org/
• PYMOL Download and License
• https://www.pymol.org/
• PYMOL Demo and Tutorial
• https://dasher.wustl.edu/bio5357/software/pymol/simple-
tutorial.pdf
• https://fitzkee.chemistry.msstate.edu/sites/default/files/boo
tcamp/2023/session-09_pymol-tutorial.pdf
• http://www.bch.cuhk.edu.hk/kbwong/pymol/pymol_tutori
al.html

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