QSAR Modeling Tutorial Using a Free QSAR Software (ChemMaster) 

Dear, Thank you for your comment. Currently, ROC curves are not provided in ChemMaster, however, we can generate it for you using other tools we have in CrescentSilico, if you can provide us more context regarding what data you want to generate ROC curve for? Generally, regression QSAR models (as in this tutorial) are not validated by ROC curves. You can contact us at: crescent_silico@outlook.com

Dear, If you mean your IC50 column name is not in the "Add Column" list choices in the Add Calculated Column Dialogue, that should be because the type of your column is not "Numerical" (to set a column datatype as Numerical, right click on the column name -> Set Column Datatype -> Numerical). Note that the column should contain only numerical values to be set as numerical.

Dear, Thank you for your comment. The HQSAR method doesn’t give an equation as the number of X-Variables (i.e. the descriptors which are the molecular fingerprints) is very large. Thus, in HQSAR research articles, the equation is not reported. As for R2, generally you should focus on the test set value, as it reflects the model ability to predict activity on new structures. The CV is for Cross Validation, which is an additional (optional) validation procedure. The R2 of CV is similar to Q2. We have a planned tutorial for the HQSAR module, so stay tuned if you are interested. Regards

Dear, Generally, public compounds databases such as ChEMBL or PubChem are used to obtain the activity of a dataset (such as EC50 or IC50). You can also obtain them from literature (e.g. research articles) that reports the compounds & their biological activity. We do provide commercial CADD (Computer-Aided Drug Design) services including providing datasets ready-to-use for QSAR modeling, or complete QSAR projects. If you are interested, you can contact us at: crescent_silico@outlook.com .

Dear Mohammed, You can use any activity type (including mIC90) to build a QSAR model (you may consider scaling the activity as well as shown in the tutorial). The built model will predict the same activity type that was used for training (thus if you use mIC90, the model will predict mIC90 values for new structures.

Dear, If you want to save the image of the figure, you can do so by right clicking on the tab name of the plot and selecting "Save Image". To change the background color of the plot, click on the plot options icon (the three vertical blue lines) -> General -> Background Color. If this doesn't help, please elaborate more on the issue. Thank you.

Thanks for the swift reply @@CrescentSilico

Yes, you can import descriptors from other sources. To do so, from the file menu select "Import Columns" then select the file. The current formats are CSV (comma separated) and Text Files (tab separated), and the first row is expected to be the header name. If this doesn't work, you can contact us to try to provide better solution.

Dear, The purpose of a random seed is to make sure the random division is the same (repeatable), the value itself is meaningless. In other words, when you enter the same random seed you get the same compounds in the training/test sets every time. It is just to control the random process to get reproducible results. You can enter any value, but each value will give you different dataset division (i.e. training/test set ids), and each value always results in the same dataset division. I hope this is clear.

Dear, For the current version, no installation process is required. After you download the ChemMaster.Rar file, right click and select Extract Here. Then open the ChemMaster folder and run the ChemMaster.exe file. If you are still unable to run the software, please contact us at crescent_silico@outlook.com and we'll send you detailed steps if required.

@@CrescentSilico thank you for the timely assistance.

Dear, if you mean the SDF file used in the video, you can find it in the description. However, if you have your own dataset of compounds, you can simply draw the structures via a software or webserver that permits drawing the structures and export them as an SDF file. If you can give us some context about what you are using and what you want to achieve, we can provide better help. Thank you.

I mean in general How to get collectively structure along with Ec 50 which software used for that, I know how to get sdf file for structure

Dear, if you want to get a dataset for a QSAR study, you can get a series of structures from a literature article that reports the structures with their activity. Or a simpler way is to download a dataset from a public database such as the ChEMBL database. If you want a dataset suitable for a QSAR study, you can contact us via the CADD services page, we can assist you in any step in QSAR modeling including dataset selection (crescentsilico.wordpress.com/cadd-services/).

Unfortunately, we currently do not have a version for Mac. However, If you need Computer-Aided Drug Design services/coding you can contact us at: crescent_silico@outlook.com .

Dear, The causes for a low R2 can result from various factors. For example, the characteristics of the dataset you are using (activity range, activity distribution, no. of points, etc.), or the type of descriptors used. If you like, you can contact us via the CADD services page, we offer extremely low-cost services, with experts in QSAR who can work on your dataset and/or provide you suitable datasets for QSAR (crescentsilico.wordpress.com/cadd-services/).

You can download the software from the official download page: crescent-silico.com/chemmaster

The SDF file contains the structures and the activity of your dataset, typically, you may draw the structures via a webserver or a software that permits drawing the structures and export them as an SDF file. If you can give us some context about what you are using and what you want to achieve, we can provide better help. Thank you.

Thank you for your suggestion, that is something we have been considering. We will attempt to do that in the near future.