I found this a few days ago (http://pubs.acs.org/doi/abs/10.1021/ci500175r). I haven't read it yet. You might want to check the paper for references to softwares or protocols.

Thank you for phrasing your question with a healthy amount of context, since there are two or more distinct ways of going about covalent docking depending on what your objective is. The CovDock method that Balder Lai mentions is ideally suited for virtual screening, whereby you're looking for candidate structures to examine in greater detail later. Another well established tool is CovalentDock which is available either as a standalone open-source program or via server (http://docking.sce.ntu.edu.sg/).

If you have already narrowed down your chemotype family of interest, however, you will get much greater analytical accuracy and insight from more brute force approaches. For example, if you know the precise chemical bond to be formed, then the best way to solve for covalently bound conformers is by explicitly creating the bound complexes and subjecting the ligand (plus immediately bound amino acid side-chain) to standard conformational search routines. Complex enthalpy will be given explicitly for all solved conformational candidates (and for some software can also include implicit desolvation effects). Entropy can be indirectly inferred by analyzing pose families. Ultimately, the most plausible conformational structure will often be the most enthalpically favorable conformer within a reasonably well populated pose family.

Once you've narrowed down the most plausible conformer(s), then you can gauge things like product stability through quantum chemical calculations (e.g., as relating to the barrier height of an internal reaction coordinate calculation). For the quantum calculations, you might decide to go with a sophisticated QM/MM method, but it will often be just as effective to simply study a representative substructure via a pure quantum calculation.

Covalant docking is having another name called metabolite docking. Where we can use active metabolites. Online software is available like DOCKBLUSTER, Metabolite docking server etc.

I pco-authored a paper in which I used Vina and Autodock do covalently dock several compounds (http://www.ncbi.nlm.nih.gov/pubmed/23474898). If you need some info drop me a message.

I use GOLD software to perform a covalent docking. It works very well and recently we have published an article in which a covalent docking procedure was used.

http://www.ncbi.nlm.nih.gov/pubmed/24909083

Moreover also in Schrodinger suite using a particular feature of Prime it is possible to perform a covalent docking.

Dear Brogi

I read your article and could understand the process of covalent docking

Thanks

Regards

You might want to use the CovalentDock program, built on the top of the source code of Autodock. An empirical model of free energy change estimation for covalent linkage formation, which is compatible with existing scoring functions used in docking, was developed while handling the molecular geometry constrains of the covalent linkage with special atom types and directional grid maps. The result tested on existing crystal structures with covalent linkage shows that CovalentDock can reproduce the native covalent complexes with significant improved accuracy when compared with the default covalent docking method in Autodock.

Recently Schrodinger integrate covalent docking mode.

Here is the attachmnet.

Thank you Arvind and Sergey for valuable information.