DNA and Protein Docking | HDOCK | Discovery Studio Visualizer | Lecture 86 | Dr. Muhammad Naveed

DNA and Protein Docking
Discovery Studio Download link: https://discover.3ds.com/discovery-st...
PDB: https://www.rcsb.org/structure/1C9U
HDOCK link: http://hdock.phys.hust.edu.cn/
Molecular Docking:    • ADMET Analysis | Pre-Clinical Drug Testing...  
QSAR Analysis:    • QSAR | 3D QSAR based Drug analysis | CADD ...  

HDOCK

1. How to provide input for docked molecules
The HDOCK server is to predict the binding complexes between two molecules like proteins and nucleic acids by using a hybrid docking strategy. Therefore, users need to provide input for the two molecule to be docked. The HDOCK server can accept four types of input for molecules:

Upload your pdb file in PDB format.
Provide your pdb file in PDB ID:ChainID (e.g. 1CGI:E).
Copy and paste your protein sequence in FASTA format.
Upload your protein sequence file in FASTA format
Only ONE type of input is needed for each molecule.

If more than one types of input are provided, the first one will be used. For the "PDB ID:ChainID" input, the user can provide one single chain ID or multiple chain IDs. For example, "1CGI:E" stands for the chain E of the pdb file of 1CGI; "1AHW:AB" stands for the chains A and B of the pdb file of 1AHW. If only a sequence is provided, the server will automatically constuct a model structure from a homologous template in the Protein Data Bank using a in-house modeling pipeline of HH Suite , Clustalw2, and MODELLER. In addition, users are also recommended to submit their own pdb file if the protein contains multiple chains, as our pipeline is currently designed to model single-chain proteins.

NOTE: For docking efficiency, it is recommended that the larger one of two molecules is input as receptor if one molecule is much larger than the other one.

Molecular Type:
"Select a type" is not needed for structure input, as the HDOCK server is able to determine a molecular type according to the input structure. However, for sequence input, users are strongly recommended to select a molecular type; otherwise, the server will guess one from `Protein', `ssRNA', or `dsDNA' based on the input sequence.
Here are the definitions of different molecular types:

2. RNA/DNA 3D structure modeling
HDOCK server now accepts sequence inputs for single-stranded (ss) or double-stranded (ds) RNA/DNA. Only the sequence of a single strand is needed, which can contain the sequence only like this

3. How to specify the binding site

The HDOCK performs global docking to predict the binding complexes between two molecules. Therefore, no information about the binding site is necessary for the docking job. However, the server also gives users the option to specify the binding site residues if such information is available, such that the predicted models will have a higher accuracy. Two types of binding site information can be provided.


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 & Vaccine designing, and Drug designing against infectious diseases. He has supervised 70 MSc. and 60 MPhil. & 01 Ph.D. students. He has published 112 Research articles with 604 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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