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How to use LigBuilder v2.0: An overview


  1. Overall architecture of LigBuilder v2.0
  2. Input format
  3. Run CAVITY
  4. Run BUILD
  5. Example for learning LigBuilder v2.0

1. Overall architecture of LigBuilder v2.0

   LigBuilder v2.0 has two main functional modules, i.e. CAVITY and BUILD. CAVITY is designed to analyze the binding pocket of the given protein and prepare the data necessary to run BUILD. BUILD is the main functional module for de novo design and results analysis.

An overview of LigBuilder v2.0 program


2. Input Format

   Most input parameters are assembled into some default parameter sets, and users could simply adjust the design strategy by loading these sets. CAVITY:The default running settings file is under the path "LigBuilderV2/bin/cavity.input".  BUILD:The default user settings file is under the path "LigBuilderV2/default/usersettings.input" and the default running settings file is in the path "LigBuilderV2/bin/build.input", please set the three files carefully before running your jobs.
   The parameter file defines the input files, the output files, and all the necessary parameters to run the program as you wish. It is in plain text, in which each line starts with a key word. You can find the detailed explanation of all the key words in the following pages of this manual.

   Example of parameter file:
      POCKET_ATOM_FILE          1db4/1db4_pocket_1.txt            //common
      INCLUDE                                ../default/default.input                  //include
      $NAME$                                  1db4                                          //predefine (only valid in BUILD)
      POCKET_GRID_FILE            1db4/$NAME$_grid_1.txt          //common
      [Extract]SEED_LIB                  10000                                         //conditional (only valid in BUILD)

   Common parameters are used for evaluation of the key words. Include parameter will guide the program to load another parameter sets. Predefined parameters will replace the corresponding string to the redefined string in all parameters inclulding these inherited from other parameter sets. In the example, the "POCKET_GRID_FILE" will be set to "1db4/1db4_grid_1.txt" for the string "$NAME$" has been replaced by string "1db4". Conditional parameters only take effect when the program executes the certain function or certain mode in the brackets. Attention: Predefine and Conditional parameters are just supported by BUILD.


3. Run CAVITY

   CAVITY has three main functions: first, analyze the binding site and prepare the information necessary for running BUILD; second, estimation the ligandability of the binding site. Third, derive the key interaction sites within the binding site and suggest a pharmacophore model.

    Synopsis of running CAVITY:

        cavity   Parameter_file

    For example:

        ./cavity  1db4.input


4. Run BUILD

   The major function of BUILD is constructing ligand molecules for the target protein by applying the fragment-based design strategy. All the molecules are developed and evolved with a Genetic Algorithm procedure. All resultant molecules will be collected in a file and reported in HTML pages.

    Synopsis of running BUILD:

        build  -Function Parameter_file [Id]

    For example:

        ./build     -Automatic    build.input

 Function List:

    Automatic:
    Automatic: Automatic design mode for one-stop drug design. With this mode, LigBuilder v2.0 will monitor all subroutines and accomplish all post-process procedure automatically. It is strongly recommend to run the design job with this mode.

    Design:
    Normal: Standard design mode. DO NOT access previous seed library. It will OVERWRITE previous result file.
    Daemon: Daemon design mode, auto resume from faults. DO NOT access previous seed library. It will OVERWRITE previous result file.
    Continue: Standard continue mode. DO access previous seed library. It will APPEND to previous result file.
    DContinue:Daemon continue mode, auto resume from faults. DO access previous seed library. It will APPEND to previous result file.

    Control:
    PAUSE: Pause
    CONTINUE: Continue
    RELOAD: Reload the parameter file(only Daemon/DContinue mode)
    EXIT: Exit
    FINISH: Force to stop design process and come to the post-process.(only Automatic mode)

    Process results:
    Process: Convert result file (LIG format) to Mol2 format
    Filter: Filtering results with structure constrains
    YScore: Estimate the ligand binding affinity of results by YScore
    Recommend: Help user to select top elites from large result sets.
    Cluster: Clustering results
    ReportCls: Report the clustering results in HTML
    ReportSyn: Report the synthesis analysis results in HTML

    Tools:
    Extract: Extract seed structures from known inhibitors( for growing and linking strategies)

    Results analysis:
    Score: Estimate the ligand binding affinity of one molecule
    Search: Searching the target substructure in the results.
    Synthesize: Accurate synthesis analysis of results

    Build database:
    ExtLibrary: Build rigid fragments library ( extracting fragments from known inhibitors, for mimcs design)
    RotLibrary: Build rotatable fragments library (extracting fragments from database)
    SynDatabase: Build reaction database
    MatDatabase: Build material database
    


5. Example for using LigBuilder v2.0

    We have provided some example files for you to practise using LigBuilder v2.0. You can find an example in the directory "example":

    1) Get receptor for RCSB PDB: Human non-pancreatic secretory phospholipase A2. (PDB entry 1db4):

            receptor/1db4.pdb            //PDB file of the protein (for CAVITY)

    2) Prepare the input file for CAVITY

            cavity.input                                       // input the receptor path
            -----------------------------------------------------------------
            RECEPTOR_FILE
                          receptor/1db4.pdb
            -----------------------------------------------------------------

    3) Run CAVITY:

            ./cavity     cavity.input

    4) Determine cavity id and estimate the ligandgability:

            receptor/1db4_surface_1.pdb           // cavity id=1 and predicted maximal pKd=8.03
            -----------------------------------------------------------------
            REMARK    5 Pedicted Maximal pKd 8.03

            -----------------------------------------------------------------

    5) Prepare the input file for BUILD

            build.input                                         // input the receptor info from CAVITY
            -----------------------------------------------------------------
            POCKET_ATOM_FILE
                  receptor/1db4_pocket_1.txt
            POCKET_GRID_FILE                    receptor/1db4_grid_1.txt
            -----------------------------------------------------------------

    6) Run BUILD:

             Start two shells first
             Shell A:
            ./build   -Automatic   build.input
             Shell B:
            chmod +x run_1db4.list                   //you'd better run the list on your cluster rather
            ./run_1db4.list                                 //than on the system node in practice

            NOTICE:
            1: It is recommended to assign each task in the list file to a computer cluster rather than run them sequentially in practice.
            2: It is not necessary to make all tasks run or finished. User can carry out tasks on different operation systems and then copy the output files to the outputting path assigned in the "LigBuilderV2/default/path.input". In this way, these tasks will NOT be monitored by the server, and please collect the output files before starting post-process.)
            3: If a subroutine lose activity as appeared in the activity list, please check the memory status first and make sure that a suitable memory strategy is used. Try to terminate the subrountie and restart it. (Sometimes the activity list would not capture the real status of subroutines, especially when the harddisk or memory load is reaching the system limit, that is, you'd better keep watching for a period of time to make sure whether the subroutines are functional or not.)
            4: Simply restart the server if it is abruptly terminated. The restarted server will reconnect to all active subroutines. DO NOT start a new server for one design task.

    7) View the report pages when accomplished

            result/report_1db4/report.html         // report page index in HTML
            result/report_1db4/images/              // directory of report pages and images

    Sample parameter files, i.e. "build.input", "cavity.input", are also included in the same directory.


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(These web pages are edited by Yaxia Yuan. Latest update: Jan. 2012)