Property Calculation FAQ

Free Molinspiration property calculation is up since January 2002 and become already well established service to the internet chemistry community (at least according to the usage numbers, reaching now about twenty thousand calculations per month).
We would like to thank all users who sent us questions or comments. 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] molinspiration.com.

May I use calculated data in a publication ?
Yes, you can use calculated properties for whatever purpose you want (publications, lectures, research reports, web documents). You can use also screenshots of our service 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 www.molinspiration.com (including adding a link to 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).

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.

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 100 per month ?
First of all, to keep the load on our server low, to guarantee you a good performance, 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 about one thousand 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 ?
Yes.

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 from which internet chemistry community may benefit. 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

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 JME 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 toolkit one can develop screening model for arbitrary activity type, starting from a set of active ligands. If this is an academic project, contact us, and we may consider to develop the model and screen molecules for you as a free collaborative project.

May I install this property calculation locally on my machine ?
Yes, we sell the property calculation toolkit 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.

I see only a gray square instead of the JME structure editor.
After submitting my molecule nothing happens and I am getting a strange script error.
JME Editor is working well with most browsers and operating systems. Problems are caused usually by incorrect settings of your browser, or too tight security restrictions imposed on some company networks. See here a structure input troubleshooting page.
You can also always use the JME editor locally as a stand-alone program to generate SMILES, and then enter your molecule it into our text-based SMILES entry interface.
To draw molecules on systems without Java support you may try our WebME Structure Editor based on Web2.0 Ajax technology.

Our company policy does not allow Java. How can I input molecules into your bioactivity calculator?
First, try to change the company policy or the company. Otherwise you can input molecules also as SMILES (as described above) or use our server based molecule editor WebME which does not require Java.

I also want to have JME with the cool substituent menu.
The substituent menu is available as a commercial add-in to the free JME. Contact us please.

March 2008, your Molinspiration team.