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EBI is an Outstation of the European Molecular Biology Laboratory. PDBe Search Services (PDBelite, PDBePro and BIObar) Sanchayita Sen, Ph.D. PDB Depositions.

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Presentation on theme: "EBI is an Outstation of the European Molecular Biology Laboratory. PDBe Search Services (PDBelite, PDBePro and BIObar) Sanchayita Sen, Ph.D. PDB Depositions."— Presentation transcript:

1 EBI is an Outstation of the European Molecular Biology Laboratory. PDBe Search Services (PDBelite, PDBePro and BIObar) Sanchayita Sen, Ph.D. PDB Depositions

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

4 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 4 Atlas Page for PDB entry 1n2c Summary

5 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 5

6 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 6 Visualising PDB entry 1N2C using Astex viewer

7 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 7 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.

8 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 8 Ramachandran Plot for PDB Entry 1n2c Finding the geometrical outliers and taking a closer look at them

9 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 9 Exploring the Sequence Information Scroll down the page to select from different options.

10 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 10 Representation of the secondary structure information throughout the entire sequence.

11 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 11 Tertiary Structure Information mapped against External Databases

12 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 12 Quaternary Structure Information using PISA

13 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 13 8 Different types of ligand present in PDB Entry 1N2C Total 22 instances of those ligands Ligand environment information is also available

14 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 14 Binding Environment for ADP

15 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 15 How does ADP interact with other residues?

16 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 16 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.

17 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 17Protein Databank in Europe25.02.201617 General Search Tools* biobar PDBeLite PDBePro *(Simple to complex searches of the PDBe Database)

18 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 18Protein Databank in Europe25.02.201618 biobar A toolbar search application for Mozilla/Netscape or firefox browsers Simple and quick retrieval of data from PDBe and 45 other Databases

19 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 19Protein Databank in Europe25.02.201619 PDBelite A simple form-based query system to search the PDBe Databases

20 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 20Protein Databank in Europe25.02.201620 PDBelite Allows combination of two or more search terms.

21 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 21 PDBelite Search Results

22 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 22

23 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 23 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

24 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 24Protein Databank in Europe25.02.201624 PDBepro A java-based flexible graphical search interface for advanced searching

25 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 25Protein Databank in Europe25.02.201625 Results from PDBepro are similar to those seen for PDBelite

26 PROTEIN DATA BANK EUROPE www.ebi.ac.uk/pdbe 26 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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