Hi all,
i want to dock protein into a receptor that has cofactor in it. I want to determine the effect of cofactor on binding. i looked around the web servers but all remove the cofactor. I found that Glide can allow the preparation. But it is commercial so cannot use.
Does anyone know about any onine server that would let the cofactor remain at the binding site and dock the other protein.
Thank you
Regards
That you try to see is difficult only by docking, it is better that you do docking without the cofactor and add it after having the complex by docking. Then, perform molecular dynamics studies with your protein-protein-cofactor complex either by dynamics simulations (AMBER, GROMACS, NAMD..etc) or using some online server to make molecular dynamics on the nanosecond scale.
Whatever said by Martiniano Bello you can proceed, through dynamic simulation we can observe the role of co-factor in protein -protein relationship.
There are several other tools too as non-commercial.
I suggest you try the HDOCK server ( hybrid algorithm of template-based modeling and ab initio free docking), ZDOCK server.
Please visit the below link for more software and tools
http://www.vls3d.com/index.php/links/bioinformatics/protein-protein-interaction/protein-protein-docking
Good Luck.
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