You can use the PELE Web Server for ligand migration studies. It's available at: http://pele.bsc.es

You can use the PELE Web Server for ligand migration studies. It's available at: http://pele.bsc.es

well, there are many way to check whether a ligand can go through a channel. You can perform docking or by steered MD you can see the dependence on the force with respect to the mutants. by steered MD you can get bach the FES too and so a kind of relative stability of the complexes.

Hi Matt,

Take a look on these servers.

http://docking.utmb.edu/

http://www.swissdock.ch/

In addition, Chimera program (http://www.cgl.ucsf.edu/chimera/) has a Autodock Vina tool that allow you running protein-ligand docking using a sever located at NBCR.

Best,

A.

Hi Matt,

Take a look on these servers.

http://docking.utmb.edu/

http://www.swissdock.ch/

In addition, Chimera program (http://www.cgl.ucsf.edu/chimera/) has a Autodock Vina tool that allow you running protein-ligand docking using a sever located at NBCR.

Best,

A.

It seems the best way is molecular dynamic study within 200 nanoseconds or more. Gromacs is a free program which is able to do that.

There are number of programs available. Autodock (http://autodock.scripps.edu/) is a freely available software. Paid softwares such as Discovery Studio from Accelrys and Schrodinger works great as well

The PELE server mentioned above by Armin looks like it's exactly what you need. But if for any reason you need more quantitative detail, you can approximately quantify the diffusion kinetics via Arrhenius statistics applied over energies derived from semi-constrained diffusion path calculations (i.e., multiple single-point molecular mechanic models that survey the energy variation as a function of constrained ligand-site distance).

You can ask around and see if anybody can do this for you: 10.1021/ct300967a

CastP server and Dogsite scorer may also be helpful to evaluate the binding pockets i.e their volume and surface area which will be helpful to determine whether a ligand will fit into it or not.

Best Regards,

in addition, still in MD flavour, you can think to perform metadyamics. in your case you will have only one CV to setup (the axis of the channel) and in one shot you get the FES for each mutant in no more than 100 nanoseconds (guessing I do not knwo your system).

I agree, that only a well-tempered metaMD study will give you an answer that doesn't leave a bad feeling in your stomach. The rest may give you a satisfying results but also a lot of doubt.

Hi Matt

You can use docking server (http://www.dockingserver.com/web)as well as protein ligand docking program such as AutoDock Tools for your work.

I would suggest Gromax with coarse grain simulation.

All the best:

Julianna

And you can try: http://bioinfo3d.cs.tau.ac.il/PatchDock/

Use pass or cpass

In case you need to detect a pocket or a channel, a group here in Barcelona has developed a code (which I have not tried) that should do it:

"fpocket : is a program to detect small molecule binding pockets and transient channels on proteins. You can download fpocket or use the webserver hosted at the RPBS."

Get it from here:

http://www.ub.edu/cbdd/?q=page/software

In addition to the previous post by Ramon Crehuet, you can use MD-Pocket that uses Fpocket program developed by my colleague P. Tuffery in order to compute the volume (and other parameter) of your cavity during the dynamics simulations (compute for a series of snapshots).

But I really enjoy and recommend the PELE webserver as a first approach.

One approach I have used to detect channel for ligands in a protein is by Vornoi Tesselation. A number of programs/scripts are available where you can use (check Tom Blundell, Luthey-Schulten and Oteypka groups' works) "out of the box". A reasonable estimate of the diameter of the ligand is needed as input. The programs output scripts for PyMol or RasMol for visualization.

You can try pocket finder tool with your protein alone and then by using normal molecular visualization tool, you can check the binding location of the ligand to the most favorable binding site.

I would also recommend Caver to find pathway of tunnel in your protein, this is nice tool that can be installed in pymol