Pharmit | Pharmacophore based virtual Drug screening | Lecture 114 | Dr. Muhammad Naveed

Pharmacophore-based virtual Drug screening.
weblink: pharmit.csb.pitt.edu/
Example Protein-Ligand complex: PDB ID: 4PPS
Results -Example:pharmit.csb.pitt.edu/search.html
Help or descriptions: pharmit.csb.pitt.edu/help.htm...
Getting Started
pharmit is a web server that facilitates virtual screening: it enables users to search for small molecules based on their structural and chemical similarity to another small molecule, with the goal of identifying those that bind to a target molecule (typically a protein receptor or enzyme). The search can take as input either a small molecule, a set of pharmacophore features (which will be subsequently described in greater detail), or both a protein and a pharmacophore or a small molecule for which a putative binding pose is known. This help follows the 4pps example, which the user may choose to follow simultaneously by clicking the link, or by other search initiation methods described below.
From PDB
A structure can be obtained directly from the PDB by entering its four-character PDB identifier in the first text box after "start from PDB" as shown in the figure below. To initiate the 4pps search using this method, the user may enter "4pps" in the box. A list of possible small molecules will be generated automatically in the second box, from which the user may choose a ligand of interest (ESE, in our case). Binding site waters may be excluded entirely, used as part of the ligand as optional pharmacophore features to include in the similarity search, or used as part of the receptor to identify which pharmacophore features of the ligand are relevant to binding (for our example, we will exclude them). To proceed with the search, the user should next choose "submit".
Visualization
After the desired structures are provided, pharmit will identify all pharmacophore features present in the ligand if a ligand structure rather than a pharmacophore query file was provided. If a receptor structure was provided, it will identify which of these features are relevant to the interaction between the protein-ligand pair using distance cutoffs between interacting features and will display only these interacting features.
Database Selection
When the user is satisfied with the query and constraints, a database to search should be selected by pressing the arrow next to the first button on the left sidebar. The options include CHEMBL20, ChemDiv, MolPort, NCI Open Chemical Repository, and PubChem, as well as several publicly available user-contributed libraries and any public or private libraries the user has personally submitted using the "create" menu accessible from the pharmit main page. Once a database is selected, pressing the search button initiates the search.
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, 6260 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).
Contact links:
1. Official website: ucp.edu.pk/member/dr-muhammad...
2. Facebook: / drmuhammadnaveed22
3. LinkedIn: www.linkedin.com/in/dr-muhamm...
4. Instagram: / prof.dr.naveed
5. Google Scholar: scholar.google.com/citations?...
6. ResearchGate: www.researchgate.net/profile/...
7. Twitter: / naveedqau
#drug #protein #ligands #pharmit #bioinformatics #drmuhammadnaveed

[@rabiapervaiz9804]

Informative video ...

[@Prof.Dr.MuhammadNaveed]

pleasures

[@danishiqbal7774]

Thanks Dr Naved All you videos are highly informative

[@Prof.Dr.MuhammadNaveed]

welcome dear

[@rawatsr854]

sir if we want to select ligand from medicinal plant library.. what should we have to do.?