Scribd
Upload
44 views8 pages

Lecture2-Structural Bioinformatics

Uploaded by

shoyo3918
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
44 views8 pages

Lecture2-Structural Bioinformatics

Uploaded by

shoyo3918
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
You are on page 1/ 8

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

You might also like