BS Research project

Question

[ayeshasahar]

Kindly guide me about the best energy minimization tools for ligands that are freely available..

[WouterDeCoster]

Please use a more informative title for your post.

Answer 1

[natasha.sernova]

See the following sites and papers:

https://www.researchgate.net/post/How_do_I_perform_energy_minimization_of_ligands_before_docking

Ligand minimization tool

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