The Instant JChem Suite, from ChemAxon, is a fantastic set of software designed for Chemists. It allows easy and simple database management to store both chemical and non-chemical data. It also contains a plethora of physical-chemical prediction and visualisation tools that can be utilised by chemists and computational based scientists alike.
I personally believe that the hidden gem within the suite is the availability of these predictive tools in the command line, found within the ChemAxon Calculator (cxcalc). In addition, calculator plug ins have also been developed by external developers. This allows you to incorporate the powerful predictive tools of ChemAxon into your larger workflows, with a little scripting.
For example, it can be used to predict the dominant protonation state of a ligand before use in MD or docking studies, with the
majormicrospecies tool. You can input and output all major file types including SDF, PDB and MOL2 using commands such as:
cxcalc [Input_File].sdf -o [Output_File].sdf majormicrospecies -H [pH] -f [Output_File_Type]:H
You can easily find the calculator plugins available and how to construct input commands using the
cxcalc –h command, or the available online information. I would thoroughly recommend looking at the tools available and how you could incorporate them into your workflows.