Dear Max,

If we agree on "docking" being "molecular docking", i.e. a computational method to behold in which mode and how strongly a small molecule (or a bigger molecule) binds to a macromolecule (majority of cases, a protein), so I would answer: no it is not. Should you need in silico prediction of such physical/physicochemical parameters, I would recommend SAR methods. The models developed by EPI can be a good option. The whole package is free-for-non-profit and easy to install on Windows machine. http://www.epa.gov/opptintr/exposure/pubs/episuite.htm

Plenty of alternatives do exist. Please refer to www.click2drug.org for a complete list of cheminformatics/modeling tools.

Enjoy!

Antoine.

Dear Antoine,

thank you for your input. I am mainly interested in using molecular docking to estimate the affinities and/or selectivities of metal-organic frameworks (MOFs) towards gaseous compounds like benzene and or formaldehyde (ppm-region).

There is not much literature around:

Korb, O., & Wood, P. a. 2010. Prediction of framework-guest systems using molecular docking. Chemical communications (Cambridge, England), 46(19): 3318–20.

http://www.ncbi.nlm.nih.gov/pubmed/20442895

Rodrigues, M. O., de Paula, M. V., Wanderley, K. a., Vasconcelos, I. B., Alves, S., & Soares, T. a. 2012. Metal organic frameworks for drug delivery and environmental remediation: A molecular docking approach. International Journal of Quantum Chemistry, 112(20): 3346–3355.

http://doi.wiley.com/10.1002/qua.24211

I will try to correlate the descriptors obtained via SAR with my experimental and theoretical results.

Dear Max, Thanks for the precision. Ho yes, I would truly recommend to go first with SAR approaches. Automated molecular docking processes are validated for small molecule-protein binding problems. Should you want to extend the domain of validity of such models, you shall embark for long research journey implying molecular mechanics parameterization, maybe multiscale modeling, plus possibly quantum mechanics calculation. That's kind of another field.

Cheers, Antoine.