Kindly guide me about the best energy minimization tools for ligands that are freely available..
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written
by
ayeshasahar •
1 answer
See the following sites and papers:
https://www.researchgate.net/post/How_do_I_perform_energy_minimization_of_ligands_before_docking
See this site and look for energy minimization:
http://www.rcsb.org/pdb/static.do?p=software/software_links/modeling_and_simulation.html
You will find at least 2 tools: AMBER (http://ambermd.org/) and
CHARMM (https://www.charmm.org/charmm/?CFID=7f7f516a-0e08-49dd-9b69-53ca5a184421&CFTOKEN=0)
Read also these articles:
AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-438
MoMA-LigPath: a web server to simulate protein–ligand unbinding
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692135/
Virtual Screening with AutoDock: Theory and Practice
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3083070/
The site below contains a lot of other links:
Click2drug
https://www.click2drug.org/directory_StructureBasedScreening.html
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