| FAQ
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Simulations Plus FAQ Section
Please select the product you are interested in by using the pull down menu on the left.
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| Question: Does ADMET Predictor work with Pipeline Pilot? |
Answer: Yes. A PP component is distributed with the program together with installation instructions.
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| Question: What input formats does ADMET Predictor accept? |
Answer: SMILES, SDF, RDF, MOL from MDL, MAC from SYBYL.
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| Question: The program refuses to run and issues the "error 75" message. What do I do? |
Answer: The ADMET Predictor installation folder and license folder must have "write" permissions set. Please reinstall the program as administrator, or have the administrator set the proper folder permissions.
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| Question: I'm having a problem with a network installation of ADMET Predictor. |
Answer: Many problems can be avoided by strictly following the installation instructions in the user manual. Especially critical is the proper network drive mapping: the map should never go deeper than two levels, i.e., no deeper than the \\servername\sharename path.
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| Question: Why are particular program features disabled (grayed out)? |
Answer: Some features are input dependent. For example, a recalculation of molecular descriptors and ADMET properties works only for SMILES inputs because only SMILES can be edited directly in the program. Many other features also depend on the number and type of licensed modules. For example, without a valid ADMET Modeler license, all modeling tabs will be disabled.
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| Question: What is the maximum number of molecules one can input into ADMET Predictor? |
Answer: The answer depends on the available RAM memory (for interactive inputs) or disk space (for batch inputs). In practice, we had no problems loading ~100,000 molecules for simultaneous display in the interactive mode and processing millions of compounds in the batch mode.
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| Question: How fast is ADMET Predictor? |
Answer: Very fast :) With almost 300 descriptors and 60 predicted properties per molecule it can still reach an impressive performance of just under 250,000 molecules per hour for typical inputs. In general, the program speed depends on input complexity, see "System Requirements" for details.
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| Question: Does ADMET Predictor put any limitations on the molecular input?
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Answer: ADMET Predictor will run and make valid predictions for any single organic molecule composed of B, C, N, O, S, P, F, Cl, Br, and I elements. The program will process molecules with other elements, but it will issue a warning about invalid predictions in these cases. Two descriptors, N_Nonorgn and N_Metal, will allow the user to easily detect and sort out these molecules. As for disconnected structures such as salts, the program will strip away monoatomic counterions (e.g., Cl-, Na+) and neutralize the remaining structure. However, disconnected polyatomic fragments are not permitted.
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| Question: Two related questions: (1) How can I save the results of an ADMET Predictor run for only selected properties and molecules? (2) I'm saving results into an Excel-compatible file but there are more than 256 columns and Excel truncates the file. What can I do? |
Answer: Currently, ADMET Predictor saves all molecular records. However, there exists an excellent mechanism for rapidly selecting either single, or groups of, properties. This, e.g., let's the user filter out zero descriptors, non-numerical variables, etc. Use the "Save Selected Columns" feature in ADMET Predictor "Save" menu.
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| Question: What is the effect of changing the default pH? |
Answer: This will affect only pH-dependent predictive models: logD and pH-specific solubility. Ionization descriptors will not be affected, _unless_ user check the option to include them, as well.
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| Question: Can ADMET Predictor run from the command line? |
Answer: By all means, yes. ADMET Predictor executable can be easily launched from the Windows command shell as well as from within batch scripts.
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| Question: I am a network version user and cannot run the program because all licenses are in use. How can I find out who is running ADMET Predictor?
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Answer: This is as easy as opening the usage log stored in the same folder with the license file. However, usage logging must first be enabled form the "Usage Logging" menu. Ask your network administrator for details.
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| Question: What is ADMET Modeler?
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Answer: It is an optional module of ADMET Predictor for automatic building of high-quality predictive models from user's data. Click here for more information.
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| Question: What predictive algorithms does ADMET Modeler employ?
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Answer: Artificial Neural Network Ensembles, Support Vector Machine Ensembles, Kernel Partial Least Squares and ordinary Partial Least Squares, Multiple Linear Regression. ANNE and SVME can be used for both regression and classification.
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| Question: How difficult is to build a model with ADMET Modeler?
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Answer: It is exceptionally easy. The program has maximum automation and, literally, it only takes pointing to the property of interest and clicking the appropriate method button to build models. More experienced users can bypass some automatic steps and finely tune this process through the Advanced Settings interface.
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| Question: Running ADMET Predictor for the first time on Windows Vista results in either of these error messages: "Cannot communicate with machnm1.exe!" or "Error – unexpected environment: contact customer support". Subsequent program unlock fails. What should I do? |
Answer: In this case try one of two solutions:
- Right-click on ADMET Predictor icon and select “Run as administrator” option under “Compatibility” tab
- Reboot computer after installation and run the program again.
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| Question: Although input compounds are processed very fast, on some computers the program seems to hang at the end while displaying the "Resetting the data grid control..." message. What causes this sudden slowdown? |
Answer: So far we have identified one reason for this abhorrent performance issue on Windows 7 platform running the AVG Free 8.5 anti-virus software. AVG significantly interfered with the TrueDB Grid control used to carry the molecular data spreadsheet. After removing AVG Free 8.5 and replacing it with its newer version 9.0, or with the highly recommended ESET NOD32 anti-virus, the issue went away.
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