Molinspiration Services FAQ

Free Molinspiration property calculation service is up since January 2002 and since become already well established resource for the internet chemistry community (at least according to the usage numbers, reaching now about eighty thousand calculations per month).
We would like to thank all users who sent us questions, comments and suggestions. Thank to this feedback we could implement already several improvements, and we will try do so also in the future.
Below you can find a short collection of the most common questions we are getting, together with the answers. If your topic is not covered, do not hesitate to send us mail to info [at]

May I use calculated data in a publication?
Yes, you can use calculated properties freely for any non-commercial activities (publications, lectures, research reports, web documents). You can use also screenshots of our tools in your presentations (thanks to people who did it already). We would like to ask you, however, to acknowledge the Molinspiration Property Calculation Service, and mention our web address (including adding a link to it in your on-line documents).
See also a growing list of publications citing Molinspiration software (be so kind and send us update if your work is not mentioned).
For more information check our Terms of Service document.

Are your logP values better than CLOGP?
CLOGP is still considered to be a "gold standard" in logP prediction. We hope, however, that our results are of comparable quality with the CLOGP ones, and useful in drug design and QSAR projects. Several Molinspiration licensees reported very good correlation of our logP values with their in-house data and with various experimental drug properties. And the statistical results (r2 = 0.944, r = 0.972, stdev = 0.428 for 12'202 molecules) also prove the very good quality of the Molinspiration miLogP model. miLogP is a model used by the ZINC database.

May I use your service in my medicinal chemistry / cheminformatics / QSAR class?
Yes, feel free to do so. Both our property prediction service and molecular database search service are used already in such classes at several leading universities. If you want to use our calculation engines locally for educational purposes, contact us please for special arrangement.

I need help with my QSAR / diversity / ... analysis. I need to design a combichem library focused on GSK-3 kinase inhibitors.
Molinspiration provides consultancy in the area of cheminformatics, QSAR, virtual screening, and drug design. Contact us please.

Why the number of calculations is limited to 1000 per month?
First of all, to keep the load on our server low, to guarantee a good performance for all users, and secondly to prevent some "experts" to use automatic scripts to calculate (and later sell) properties for large molecular databases. If you need more data for your research project, let us know, and we may consider to increase the limit for your IP address (or even to calculate the data for you, if you will send us molecule SMILESes). If you need to calculate data for large number of molecules on a regular basis, purchase our property calculation engine.

Why are you providing this service for free?
To do daily a good deed (actually currently few thousands of them daily), to support internet chemistry community, to provide a test bench for our tools (you would not believe which strange molecules some people submit), and to advertise Molinspiration products.

Will this service stay free also in the future?

I collected set of structures of nuclear receptor ligands and want to make this available at the internet. I'd like to include also calculated molecular properties.
We support projects beneficial to the internet chemistry community. Send us your database (SMILES or SDfile) and we will calculate properties for the molecules. Eventually for single structures you may add a "property calculation link" to our site with molecule SMILES as an input (please contact us before doing so), for example

Calculated properties for Moclobemide.
Why my calculation for ciprofloxacin / 4-Cl-Ph-CO-NH-Me / C8H6N2O2 failed?
You can draw your structures either with help of JSME JavaScript editor (that works also on touch devices and mobile phones), or enter molecule SMILES into the text input box. Input of structures by name, or molecule formula is not supported (although we have been quite pleased some time ago by the text entry "thank you very much"). If you want to find a SMILES corresponding to the name, try PubChem.

I am pasting SMILES from PubChem, but still getting errors.
Check that there are no newlines and spaces in the SMILES, or that the end of SMILES string is not truncated. We can see this type of errors quite often in our logs.

How should I correctly input nitro derivatives and N-oxides?
Input nitro groups, N-oxides and related structures with pentavalent nitrogen as shown below. You may use the "y" keyboard shortcut in JSME to input the nitro group. The form with a polar bond is also accepted. Do not enter this type of molecules with the -OH bond (this is a quite common error according to our logs) !

How the different counterions affect calculated values for the charged structures?
When entering multipart SMILES in the text entry box, the program automatically selects the main part for which properties are calculated. We recommend to enter molecules as singlepart, non-charged structures.

I need to virtually screen my structures for specific activity on GPCR imidazoline receptor.
With our virtual screening engine one can develop screening model for arbitrary activity type, starting from a set of active ligands.

May I install this property calculation locally on my machine?
Yes, we sell the property calculation engine which powers this service. You can use it as a web engine (we can offer help with the web deployment) or use it in a batch mode to calcule properties for hundreds of thousands molecules. You are not allowed, however, to provide property calculation services publicly on the internet.
Alternatively, you may consider purchasing Molinspiration Property Calculator which allows easy interactive calculation of molecular properties on your desktop.

Which other interactive services do you plan to install at your site?
Well, that depends also on you. Which other such services / tools would you find useful? Let us know, and we may consider to implement additional service getting the most "votes".
Probably the next tool will be an interactive tautomer generator.

What about confidentiality of structures I am submitting to your servers?
All processed structures are logged on our servers and logs periodically checked to identify possible errors in Molinspiration software. We have, of course, no information about identity of users (with exception of the client IP address). If you need to process confidential structures, you may contact us for free local evaluation of our tools, and if you are satisifed to purchase Molinspiration software.

Nov 2016, your Molinspiration team.