how to automaticly Spilit dataset of ligands to single pdb file?
is there any scripts for that? i have been tried openbabel software previously.
Mr. Ranjbar,
Your question assumes that you most probably have not seen "Hyperchem", because of it is fully automatized program package. It is even more automatized, then Gaussian one (www.gaussian.com).
You have to draw your molecular skeleton; then H-atoms are added by: 1. "Build"-"Add H"; 2. "Build"-"Add H, Model Build". Thus you can draw set molecules (only ligands, metal-organics; inorganics).
The optimization you can do, using a set methods shown in "Setup" options. The final step is only to compute the molecules via "Compute" option.
Hope you get some useful information from the following.
The Next-generation Structure-based Drug Design System
Homology Modeling for HyperChem
Docking Study with HyperChem
Virtual Screening System
http://www.molfunction.com/script.htm
Virtual Screening System (tentative name)
http://www.molfunction.com/technology.htm
Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443793/pdf/CTMC-14-1923.pdf
Drug Design Laboratory
http://nova.disfarm.unimi.it/cms/index.php?Software_projects:VEGA_ZZ:History
if you go thru the above link you come across 'evaluate ligand - receptor interactions by different PLANTS scoring functions.'
Linux4Chemistry (this link provide several programs choose that suits you)
http://www.linux4chemistry.info/
Super models in the laboratory. Nature 400, 485-486 (29 July 1999) | doi:10.1038/22818
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