Hello,
I'm trying to do virtual screening with multiple(up to 100,000) ligands.
I've seen, and used many free docking tools, such as autodock4 and autodock vina, however I've never encountered free tool for ligand pre-preparation.
I'm trying to process multiple ligands at once, and give modifications such as protonated/de-protonated states regarding the pH and temperature sets.
I've been told that commercial software from Schrodinger has such functions, but before I purchase one, I'm looking for availability of free package.
Please let me know if there is any :)
Thanks
You may use OpenBabel (http://openbabel.org/wiki/Main_Page). It is an open source toolbox.
I would recommend iGEMDOCK for virtual screening of ligands with detailed amino acid analysis. It is offline tool freely available for ligand screening under different categories.
Dear Eunsoo Yu
You can preprocess your data with Chem Axon package, you can make any modeification and after you can use your software to perform the VS.
Also you cans use for example OpenBabel to do this with the advantage that it is free.
best regards
We have developed a pipeline for ligand preparation to virtual screening called poap ..published in computational biology and chemistry. ..i guess will be useful. https://doi.org/10.1016/j.compbiolchem.2018.02.012
1) Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening .
2) Frog2 server
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