Frequently Asked Questions
PASS predicts with high probability that my compound should have a particular biological activity (for example, angiogenesis inhibitor). Does it mean that my compound is angiogenesis inhibitor?
- PASS estimates the probability that your compound is belonging to the particular classes of active compounds (in your case - to the angiogenesis inhibitors). This helps you to identify the particular biological assays, in which your compounds should be studied. You may conclude that your compound is angiogenesis inhibitor only after the appropriate experimental confirmation.
Results of PASS prediction for my compound appear contradictory: the compound is predicted as 5 Hydroxytryptamine 1B antagonist with probability Pa=0.653 and as 5 Hydroxytryptamine 1B agonist with probability Pa=0.587. How should I interpret these results?
- It means that your compound has affinity to 5 Hydroxytryptamine 1B receptors; however PASS cannot identify its intrinsic activity. You should determine this activity in the experimental assay.
What are the differences between the free PASS Online service and commercially available version of PASS?
- There are many differences between the free PASS Online service and commercially available version of PASS. Some of them are presented below.
(1) In PASS Online service, to get a prediction, one should send the chemical structure and obtain the prediction results via Internet that might lead to disclosure of confidential information. Commercially available version of PASS (PASS) is a desktop application, which, being used in house provides the complete security of the chemical structures and prediction results.
(2) PASS Online accepts only one structure at time, as a separate MOLfile, and presents the prediction results at the user's display, which can be saved in a "copy-paste" mode. PASS allows making prediction for a set of structures presented as SDfile; to save prediction results in different formats and analyze them by PharmaExpert or using standard Excel tables.
(3) PASS Online does not correspond to the latest version of PASS; therefore the number of predictable activities and the number of biologically active compounds used for training are significantly less. With a commercial product the user always has the latest PASS version, which provides the best prediction results achievable at a particular moment of time.
(4) In PASS Online the list of predictable activities and the SAR knowledgebase are fixed. In a professional version of PASS the user can use its own training set with new proprietary compounds and novel activities, to re-train the program and to obtain the exclusive in house SAR knowledgebase.
If you wish to get more information about PASS and PharmaExpert software, please, write us and we will send you the requested information soon.