PDBsum | LIGPLOT | Protein-Protein Interactions analysis | Lecture 111

PDBsum | LIGPLOT | Protein-Protein Interactions analysis | Lecture 111 | Dr. Muhammad Naveed

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PDBsum:
weblink: www.ebi.ac.uk/thornton-srv/da...
Results -Example: www.ebi.ac.uk/pdbsum/rex1&cod...
PDBsum is a pictorial database that provides an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank (PDB). It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of the interactions between them.
1. Description
The PDBsum is a pictorial database that provides an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank (PDB).
It shows the molecule(s) that make up the structure and schematic diagrams of their interactions. Extensive use is made of the freely available RasMol, JSmol, and PyMOL molecular graphics programs to view the molecules and their interactions in 3D.
A new addition is the inclusion of over 23,000 Alpha Fold predicted models for all human protein. These are coloured by the confidencee in the accuracy of each part of the model, using the same colouring scheme as on the Alpha Fold website.
2. Search
Entries are accessed either by their 4-character PDB code, or by one of the two search boxes provided on the PDBsum home page:
text search, which searches a given string against the TITLE, HEADER, COMPND, SOURCE and AUTHOR records in the PDB. For a fuller description of the options that the text search offers, see here.
sequence search, which performs a FASTA search of a given protein sequence against the sequences of all proteins in the PDB. The top hits are listed with links to their PDBsum pages.
3. Browse
You can also use any of the Browse options given on the PDBsum home page:
Highlights - which tabulates some of the extreme structures in the database in terms of age, size, etc
List of PDB codes - which lists all entries by their 4-character code
Het Groups - lists all Het Groups in the PDB with links to the structures that contain them
Ligands - as for Het Groups, but considering each bound molecule as a separate entity
Drugs - lists the drug molecules found in structures of the PDB.
Enzymes - lists all enzyme structures in the PDB classed by the hierarchical E.C. numbering scheme. Also known as the Enzyme Structures Database.
4. Information presented on the PDBsum pages
The information given on each PDBsum entry is spread across several pages, as listed below and accessible from the tabs at the top of the page. Only the relevant tabs will be present on any given page.
Top page - summary information including thumbnail image of structure, molecules in structure, enzyme reaction diagram (where relevant), GO functional assignments, and selected figures from key reference
Protein - wiring diagram, topology diagram(s) by CATH domain, and residue conservation (where available)
DNA/RNA - DNA/RNA sequence and NUCPLOT showing interactions made with protein
Ligands - description of bound molecule and LIGPLOT showing interactions made with protein
Prot-prot - schematic diagrams of any protein-protein interfaces and the residue-residue interactions made across them
Clefts - listing of top ten clefts in the surface of the protein, listed by volume with any bound ligands shown
Links - links to external databases.
About Dr. Muhammad Naveed
(HoD, Biotechnology, University of Central Punjab, Lahore)
With distinction, Dr. Muhammad Naveed obtained a Ph.D. degree in Biotechnology (Genomics & Bioinformatics) from Quaid-e-Azam University, Islamabad. He has won Ph.D. indigenous & IRSIP scholarships from HEC. He has done Pre-Doc research at the University of Ghent, Belgium. HEC awarded him the best Ph.D. (IRSIP) Scholar of the Year in 2013 & QAU honored him as a “Distinguished Alumni” in 2017. He is doing research projects in Bioinformatics, Molecular Biotechnology, Nano-informatics and vaccine designing, and Drug designing against infectious diseases. He has supervised 90 MSc. and 80 MPhil. & 02 Ph.D. students. He has published 152 Research articles with 1186 impact factors, 6060 citations, 01 book, 06 book chapters, and filed 05 Patents. He was awarded the distinguished “Researcher of the Year” in 2016 (UoG) and 2018, 2019 & 2021 (UCP).
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