How to use the FAF-Drugs web-server.

This page is dedicated to describe in detail how to use and run FAF-Drugs2 hosted on the Mobyle Portal.

Here is available a short movie tutorial which details how to easily run FAF-Drugs.

If you need more precise informations about running FAF-Drugs and/or customizing your filtering process, you can follow up the indications below.


» Accessing to the service.

  • Go to Mobyle Portal.
  • In the left panel, select in the Programs Section » Drugs » ADMETox » FAF-Drugs2 » FAF-Drugs2
  • Optionally, at the top right, sign in your email to be notified when your job is launched and finished.

    Additionnaly, you can register for an account, which enables you to store your bookmarked data and results on the server, without any time limit.
    You can also connect using the same e-mail and password from any place.

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  • » Optional Services :
    • In the » FAF-Drugs2 Section, you can see 2 additional services, namely Bank-Formater and Filter-Editor.

      » Bank-Formater is a tool for preparing your compound library in order to properly process the job, especially regarding the Symyx SDF file format recommandations. It takes Smiles and SDF file formats as input, and generate exclusively an acceptable SDF file.
      In order to launch the process, you need to paste or upload your own file.
      Before running the program by clicking on the RUN button, be sure that you had selected the file format of the input file (1).
      When the process is finished, the SDF file generated can be automatically redirect, as input file, to the FAF-Drugs2 service by using the drop-down menu (1), select FAF-Drugs2 (input file), and click on the further analysis (2) button


      » Filter-Editor is a tool to design your own filtering parameter file. To this end, you can enter your parameters in the dedicated several areas, and click on the RUN button:
      It will automatically updating the internal standard parameter file with your own filtering ranges.
      To proceed FAFDrugs2 process with those customized parameters, you need to use the drop-down menu (1), select FAF-Drugs2 (inputParmsFile), and click on the further analysis (2) button.
        As you can see, your values that will customizing the filtering ranges are displayed.

» Testing the service.

  • You can test FAFDrugs2 by using an embedded demonstration mode.
  • If you click on the corresponding radio button (1), and running the program (2), a small internal SDF file containing 9 compounds will be processed.

  • WARNING !! : If you have tested FAF-Drugs before running your own compounds, be sure you have deselected the testing (1) radio button !!


» Input Files, Options and Parameters.

Note: According to MDL Information Systems - Symyx Technologies Structure Data Files guidelines, compounds collection must be in a valid SDF file [17].
It means that each header block of molecules must be composed by 3 lines, the first one must contain the molecule name or the ID tag in a one continuous pattern.
OpenBabel works upon that guidelines, so if no name/ID is specified, you must perform this adjustment.
To this end, you must firstly check if your input file is in an acceptable format, and if needed, you can use the Bank-Formater tool previously described.


  • You have 2 possibilities to enter your data, both of these being selected by clicking on the corresponding radio button:
    • (1). Copy/Paste: Simply copy and paste your SDF file in the text area.
    • (2). Local file: Select a local file stored on your computer and upload it.


  • Several filtering options are available (1) :
    • 1. In-House or published Physico-Chemistry filters:

      • You can access it by using the drop-down menu to differents filters, ranges are detailed on the filter dedicated page:
          • » in-house drug-like and lead-like filters, according to several publications [19],[26-31].
          » Probe-like filter, according to Workman et al. [32].
          » REOS filter, according to Charifson et al. [33] and Walters et al. [34].
          » Lipinski-RO5 filter, fitting the Lipinski's Rule-of-five.
          According to Lipinski et al. [13], that filter only computes the 4 descriptors: logP, Molecular Weight, H-Bond Donors and Acceptors, and checks how many values are violated. According to the seminal work, two violations are allowed, but in agreement with many references we have deliberately lowered the number of violations to one.
          » Rule of Three filter, according to Congreve et al. [35]. That filter could be useful when constructing fragment libraries for efficient lead discovery. It involves logP, Molecular Weight, H-Bond Donors and Acceptors, number or rotatable bonds and tPSA.
          » ZINC filter, according to Irwin et al. [24].
          » CNS filter, according to Jeffrey et al. [36], which give some filtering guidelines in order to selecting only the compounds that could enter the Central Nervous System.
          » Inhaled - Respiratory filter, according to Ritchie et al. [25], which give some filtering guidelines in order to selecting only the compounds that could be nasal/inhalatory bioavailable.
          » Oral filter, according to Ritchie et al. [43] and Lipinski et al. [13], which fit on the oral absorption estimation ranges employed to design the dedicated radar plot (see below the Full Results page description).

    • 2. You can choose which method will compute the logP values (1) between the embedded logP method of OpenBabel [3] or the XLOGP3 program under license agreement established between our lab and Pr R. Wang [5].


    • 3. Then, you can apply, or not; in one hand, (1) the detection of undesirable moieties (functionnal groups detected are detailled in the Substructure Searching section), in another hand, (2) the detection of the 480 Pan Assay INterference compoundS (PAINS) according to Baell et al [23], see Supporting Info.


» Running the service.

  • You can now run FAFDrugs2 process by clicking on the Run button (1).
  • Clicking on the Reset (2) button will clear all input data you entered, and stop the process.

The first time you will run FAF-Drugs, you will have to enter a security string. Don't worry, you only have to do this the first time you run FAF-Drugs.

  • Once you have submitted your data, a new job will be created, and you will be redirected to this new job tab page as shown bellow.
    Two possibilities can be possible:
      » The job is running and you just have to wait for results to appear.

      At that stage, if you had previously sign in your email, you may be notified by an email message that your job was launched and is running.
      You will receive another email message when it will be finished.
      » The job is pending and you have to wait until it will be launched.

» Output Description.

  • In Mobyle, once your job will be finished, you will be redirected to the mobyle results page. This results page is shown on the picture below.

    Differents results pages are actually contained in several files and all are downloadable on your own computer using the Save button (1).

    You also have the possibility to bookmark the result page using the Bookmark button (3) (enter the bookmark name in the field on left), in order to access to the results any time you need.

    The results could be displayed in two ways, a “web-based“ way, or alternatively, by editing the several “text-formats“ files (after having downloading them (1)) in any text editors and/or any spreadsheet software, especially for the “.csv“ files


  • Before developping the “web-based“ way, as explain before on the Mobyle results page you will find several windows (each time associated with a file that can be saved on your computer):
  • 1. The links for downloading the ending filtering files (Accepted.sdf, Intermediated.sdf and Rejected.sdf).
  • 2. The "results.csv" file which gather all physico-chemistry results of the filtering process.
  • 3. The "groups.csv" file which gather all the results of the substructures/undesirables moieties searching process ( if the dedicated option was activated)
  • 3. The "pains.csv" file which gather all the results of the PAINS searching process ( if the dedicated option was activated)
  • 4. A simple window summarized the filtering process.
  • 5. The standard output of FAFDrugs2 (i.e.terminal display)
  • 6. Each separate pictures wich are displayed in the “web-based“ version.


  • Regarding the “web-based“ analysing procedure, just click on the full screen view button (2) to reach the following free-handly graphical web-based interface "FAFDrugsHTMLReport" which is divided in 2 sections :

    • 1. The Summary Page, divided in 5 sections:

        » A summary section which proposes, in one sub-section, the links for downloading the various ending filtering files and in another sub-section which briefly details the filtering results.


        » The distributions diagrams of the values of logP, tPSA, Molecular Weight, Rotatable Bonds, H-Bonds Acceptors and Donors computed for the compound libray analyzed.


        » If the groups detection option is activated (please see section Options and Parameters above), here is shown a pie chart of the chemical substructures mostly detected in the analysed database. Only the moieties which their detection represents at least 1% are considered. This is the reason why on the graphic the total is not equal to 100%.


        » The table containing all compounds analysed with their ADMET filtering state. Each column is sortable. A colouring is employed to materialize each compound status: green for "Accepted", blue for "Intermediate" (special status involved when the substructures and/or PAINS searching is activated. It means that special flagged moieties have been highlighted, please see Substructures and PAINS searching sections.), and red for "Rejected".
        Each compound results could be detailled by clicking on its ID. It will open a new internet browser window.
        Please, see below section 2.

        » Finally all filtering input parameters employed for the current process.

    • 2. The Full Results page for one specific molecule (2).

      On this page could be found :

      • all values computed (1).

      • if it is the case, a list of all encountered problems (2) justifying the classification of the compound in the Rejected or Intermediated groups.

      • a 2D depiction picture (3) of the compound selected (based on ChemAxon molconvert tool [22]).

      • a chemical property space (4) of an in-house library of 466 orally bioavailable compounds extracted from the DrugBank database (http://www.drugbank.ca). That graph is obtained by applying the PCA (Principal Component Analysis) of the 14 principal physico-chemical descriptors of these molecules (blue). Then, the compound analyzed (pink) is projected, in the same conditions, on the same chemical space. To see the correlation between the original descriptors and the new space, click here.

      • a radar plot (5) representing an oral absorption estimation:
        The compounds values are materialized by the blue line, which should fall within the optimal green area.
        The white area is the extreme maximun zone while the red one is the extreme minimum zone. These zones are obtained with the following descriptors ranges: logP (-2 to 5), Molecular Weight (150 to 500), tPSA (20 to 150), Rotatable Bonds (0 to 10), H-Bonds Acceptors (0 to 10) and Donors (0 to 5).
        Note that a special filter which fit on these properties, named oral filter, could be applied in FAF-Drugs2
        (please see filters section).
      Note: (3),(4),(5) pictures can be enlarged by clicking it.