1) Please explain, How create a protein structure by docking studies
2) How to select a target protein
@Dr Jagan Nadipelly: Hello Doc. , first of all you need to have structure of the protein which you can download from PDB database (http://www.rcsb.org/pdb/home/home.do) search for the protein you want to target . it is not always necessary that you have the crystal structure of the protein, thus you can do homology modelling with various online and offline softwares (http://zhanglab.ccmb.med.umich.edu/I-TASSER/, http://raptorx.uchicago.edu/) and for that you need to have the sequence of the closely related protein which you can find by doing BLAST(https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) .Once you are done with the structure, you select highest scoring binding site on protein to target ligands, the binding of ligand generates a score (docking score, Glide score, MMGBSA, MMPBSA), typically you select the ligand with lowest score. docking can be done by various online and offline softwares which are again free as well as paid. these are some freely available softwares (http://autodock.scripps.edu/, https://bioinfo3d.cs.tau.ac.il/PatchDock/,http://www.swissdock.ch/)
considering you are new to this please go through this article
http://www.sciencedirect.com/science/article/pii/S1074552103001947
Check out our paper - Anna E. Lohning, Stephan M. Levonis, Billy Williams-Noonan, and Stephanie S. Schweiker, A Practical Guide to Molecular Docking and Homology Modelling for Medicinal Chemists, Current topics in medicinal chemistry, 2017
Hope this helps.
Kindly,
Stephanie
Thank you very much for your valuable reply - Rajesh Pal and Stepanie S. Schweiker
Welcome Doc., Pls let me know if you have additional questions/comments :)
Please go through this book "Computational Drug Design: A Guide for Computational and Medicinal Chemists"
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