Please help me with any webserver tools and software to process carbohydrate/monosaccharide - ligand in silico docking
Fariba Heidarizadeh
GlycanDock: This is a webserver tool that can be used for docking carbohydrate ligands with protein receptors. It uses AutoDock Vina as the docking engine and can handle a variety of glycan structures. You can access GlycanDock at: http://bmm.cancerresearchuk.org/~glycandock/ LIGSITEcs: This is a software tool that can be used for predicting the binding sites of proteins and performing ligand docking. It includes a feature that can identify carbohydrate-binding sites and has been used successfully for carbohydrate-protein docking. You can access LIGSITEcs at: http://www.ligsite.org/ GLIDE: This is a commercial software package that includes a docking module for predicting ligand binding to proteins. It has been successfully used for carbohydrate-protein docking and has a user-friendly interface. You can access GLIDE at: https://www.schrodinger.com/products/glide AutoDock Tools: This is a software package that can be used for preparing protein and ligand structures for docking with AutoDock Vina. It includes a feature for building carbohydrate structures and can handle a variety of formats. You can access AutoDock Tools at: http://autodock.scripps.edu/resources/adt CARLIT: This is a webserver tool that can be used for docking carbohydrate ligands with protein receptors. It uses a database of precomputed docking poses and can be used for virtual screening of carbohydrate libraries. You can access CARLIT at: http://redpoll.pharmacy.ualberta.ca/CARLIT/
Here are some webserver tools and software that you can use to process carbohydrate/monosaccharide-ligand in silico docking:
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Sargol Mazraedoost
AutoDock Vina: AutoDock Vina is a popular molecular docking software that can be used for docking of carbohydrates or monosaccharides with other molecules. It uses an efficient search algorithm to explore the conformational space of the ligand and protein, allowing for accurate predictions of binding modes and affinities. SwissDock: SwissDock is a web server for protein-ligand docking that allows for the docking of small molecules such as carbohydrates. It uses a combination of docking algorithms and scoring functions to predict the binding affinity and pose of the ligand with the protein. HADDOCK: HADDOCK is a widely used web server for macromolecular docking, including protein-carbohydrate docking. It uses a combination of information from experimental data, protein-protein interactions, and protein-ligand interactions to generate accurate predictions of the binding mode and affinity. GlycoDock: GlycoDock is a web server designed specifically for the docking of glycans and glycoproteins with other molecules. It uses a combination of molecular dynamics simulations and energy minimization to generate accurate predictions of the binding mode and affinity. FlexAID: FlexAID is a software package for the molecular docking of small molecules, including carbohydrates. It uses a combination of protein flexibility and ligand conformational search algorithms to generate accurate predictions of binding modes and affinities. AutoDock Vina: http://vina.scripps.edu/ SwissDock: https://www.swissdock.ch/ HADDOCK: https://wenmr.science.uu.nl/haddock2.4/ GlycoDock: https://glycodock.glycosmos.org/ FlexAID: https://bioserv.rpbs.univ-paris-diderot.fr/services/FlexAID/
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