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PDBe Search Services (PDBelite, PDBePro and BIObar)

PDBe Search Services (PDBelite, PDBePro and BIObar). Sanchayita Sen, Ph.D. PDB Depositions. Contents. Exploring the PDBe to find information about a particular PDB entry of interest – the atlas pages Performing a more general and simple search – using BIObar

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PDBe Search Services (PDBelite, PDBePro and BIObar)

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  1. PDBe Search Services (PDBelite, PDBePro and BIObar) Sanchayita Sen, Ph.D. PDB Depositions

  2. Contents • Exploring the PDBe to find information about a particular PDB entry of interest – the atlas pages • Performing a more general and simple search – using BIObar • Querying the database using multiple search options – using PDBeLite • Advanced Query options – using PDBePro

  3. PDBe Home Page http://www.ebi.ac.uk/pdbe Insert a PDB ID code that is publicly available All Tutorials and Handouts Available

  4. Atlas Page for PDB entry 1n2c Summary

  5. Visualising PDB entry 1N2C using Astex viewer

  6. Looking into the environment of a particular ligand • manipulate the distance between the ligand and its neighbouring residues • Shows both water and other amino acid residues/ligands in the environment • Clicking on each of the residues will zoom into the structure enabling a closer look • Contacts can be screened based on type of interactions.

  7. Ramachandran Plot for PDB Entry 1n2c • Finding the geometrical outliers and taking a closer look at them

  8. Exploring the Sequence Information Scroll down the page to select from different options.

  9. Representation of the secondary structure information throughout the entire sequence.

  10. Tertiary Structure Information mapped against External Databases

  11. Quaternary Structure Information using PISA

  12. 8 Different types of ligand present in PDB Entry 1N2C • Total 22 instances of those ligands • Ligand environment information is also available

  13. Binding Environment for ADP

  14. How does ADP interact with other residues?

  15. Information available from the atlas page of a PDB entry • Experiment Type • Source of the macromolecule • Citation information • Visualisation tools • Corresponding sequence information from Uniprot Database. • Taxonomy Information • Secondary Structure information • Quaternary structure information derived from PDBe-PISA • Ligand information derived from PDBe-chem and PDBemotif • Download the PDB file and Structure factor file.

  16. General Search Tools* biobar PDBeLite PDBePro *(Simple to complex searches of the PDBe Database) 17 09.10.2014 Protein Databank in Europe

  17. biobar A toolbar search application for Mozilla/Netscape or firefox browsers Simple and quick retrieval of data from PDBe and 45 other Databases 18 09.10.2014 Protein Databank in Europe

  18. PDBelite A simple form-based query system to search the PDBe Databases 19 09.10.2014 Protein Databank in Europe

  19. PDBelite Allows combination of two or more search terms. 20 09.10.2014 Protein Databank in Europe

  20. PDBelite Search Results

  21. Describing Complex Searches (ADVANCED USERS) • We want to allow the user to entirely control their query • Since HTML forms are inherently static, we'll use an applet to provide a dynamic "form" that will let the user: • choose the fields to be searched • specify the relationships between search fields • choose the result fields and how results are presented • perform "complex" sub-queries e.g. SSM, FASTA • MSDpro uses an applet for constructing queries and a server to execute them • The user describes their query entirely graphically, including logical operations such as AND, OR and NOT

  22. PDBepro A java-based flexible graphical search interface for advanced searching 24 09.10.2014 Protein Databank in Europe

  23. Results from PDBepro are similar to those seen for PDBelite 25 09.10.2014 Protein Databank in Europe

  24. Acknowledgements • BIObar – Dr. Jawahar Swaminathan • PDBelite – Dr. Sameer Velankar, Dr. John Tate • PDBePro – Dr. Sameer Velankar, Dr. John Tate Questions? msdhelp@ebi.ac.uk

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