LIGPLOT for protein-ligand interactions | Installation and working | Lecture 80 |Dr. Muhammad Naveed

Описание: LIGPLOT for protein-ligand interactions
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LigPlot+ is a graphical front-end to the LIGPLOT and DIMPLOT programs. The plots generated by these programs can be interactively edited on screen and then written to a PostScript file for printing or conversion to various image formats. Additionally, you can superpose related LIGPLOTs to highlight similarities and differences between related proteins binding the same/similar ligand, or the same/similar ligand binding to different proteins.

LIGPLOT - automatically generates schematic diagrams of protein-ligand interactions for a given ligand in a PDB file.
DIMPLOT - plots interactions across a selected protein-protein or domain-domain interface.

The first time you run LigPlot+ on your computer, you will need to define several paths and directories so that the program knows where to find things like PDB files, the Het Group Dictionary and the RasMol/PyMOL programs (if you have them). LigPlot+ will detect that it is being run for the first time and will pop up an entry-form, described in the section below, for you to fill in.

i. PDB paths
PDB files are most conveniently identified simply by the 4-character PDB code or identifier. If your system contains one or more locations where PDB files are stored, you can define a "template" path which will allow LigPlot+ to find the relevant PDB file from its 4-character code alone. The files can be gzipped or not.

Alternatively, if you are connected to the internet when you run LigPlot+, the required file can be retrieved by ftp from a given ftp site.

The 4 characters of the PDB code in each template are represented as abcd. These appear in the template within square brackets.

For example, the template

C:/roman/pdbsum/pdb/pdb[abcd].ent
means that, for example, PDB code 1ral would be translated as:
C:/roman/pdbsum/pdb/pdb1ral.ent
Similarly, the ftp template
ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/structures/divided/pdb/[bc]/pdb[abcd].ent.gz
would map to PDB code 1ral as:
ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/structures/divided/pdb/ra/pdb1ral.ent.gz
Note that here the PDB files are stored in subdirectories whose names correspond to the middle part of the PDB code (here shown as "[bc]").
The above ftp address retrieves gzipped PDB files from the PDBe ftp site at the EBI. A full list of possible ftp addresses is given below:

PDBe ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/structures/divided/pdb/[bc]/pdb[abcd].ent.gz
PDBj ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/pdb/[bc]/pdb[abcd].ent.gz
RCSB PDB ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/[bc]/pdb[abcd].ent.gz
You can add others.
ii. The Het Group Dictionary
LigPlot+ gets its information about ligand molecules from the Het Group Dictionary. This defines the atom names, connectivities and bond orders of every Het Group in the PDB. You can download a copy of this dictionary from the wwPDB at:
ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif
It is a good idea to download it regularly to always have an up-to-date copy.


About Dr. Muhammad Naveed
(Associate Professor, 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 & Vaccine designing, and Drug designing against infectious diseases. He has supervised 70 MSc. and 60 MPhil. & 01 Ph.D. students. He has published 102 Research articles with 504 impact factors, 2000 citations, 01 book, and 03 book chapters. He was awarded the distinguished “Researcher of the Year” in 2016 (UoG) and 2018, 2019 & 2021 (UCP).
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