Do you know of a good software or web server tool that helps doing docking of proteins with rather large glycans? An example I'm interested in is tens of dimers of sugars (or similar), docked to proteins. I know sugars are somewhat hard to study because of their flexibility, but I was wondering if there was something out there for this case?
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3$\begingroup$ Docking software and server are specialized in small molecules, peptides and proteins. Maybe you can use a different method to study the interactions between the proteins and glycans (ex. semiempirical software MOPAC using MOZYME keyword, Fragment Molecular Orbital inside GAMESS-US or go directly to molecular dynamics). $\endgroup$– Camps ♦Commented Aug 8, 2020 at 19:19
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The main issue here is not about the type of ligands (glycans) even when it is known that there are force fields that are specific for each type of system. The main issue is about how flexible and big is the ligand you are using to dock.
The GLIDE software, for example, has been increasing the number of atoms and rotatable bonds it is able to handle. Since 2015-1 release, it can handle ligands with up to 500 atoms and 100 rotatable bonds (versus 300 and 50 in previous releases).
In case of AutodockVina software, the default values are 2048 atoms and 32 torsions, but these values can be changed in the variables MAX_ATOMS and MAX_TORS in the constants.h.
There are some webservers for docking, but I am not aware of their limitations. Some of them are SwissDock, Webmina, DockBlaster, and MTiAutoDock 1.0, among others.
If this software aren't able to treat your system, you can use a different method to study the interactions between the proteins and glycans, ex. semiempirical software MOPAC using MOZYME keyword, Fragment Molecular Orbital inside GAMESS-US or go directly to molecular dynamics.
