1. Overall architecture of LigBuilder V3
2. Input format
3. Run Cavity
4. Run Build
5. Example for learning LigBuilder V3

1. Overall architecture of LigBuilder V3

An overview of LigBuilder V3 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 "LigBuilderV3/build/cavity.input".  Build:The default user settings file is under the path "LigBuilderV3/build/usersettings.input" and the default running settings file is in the path "LigBuilderV3/build/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.

  Special keyword in parameter file of build:

   INCLUDE                                                          // Include other parameter file to current position
   $VariableName$                                                 // Predefined global variable in the parameter file
   [Function][TargetNum]Keyword[TargetID]         // Function: the keyword is only valided for specific function
                                                                             // TargetNum: the keyword is valided for N targets design
                                                                             // TargetID: the keyword is valided for specific target

  Some examples:

   INCLUDE                                ../default/default.input                   // All keywords in file ../default/default.input are include
    $NAME$                                  1db4                                          // NAME is defined as 1db4
   POCKET_GRID_FILE            1db4/$NAME$_grid_1.txt          // Now the keyword is 1db4/1db4_grid_1.txt, because $NAME$ is defined as 1db4
   MINIMAL_PKD                          5                                           // MINIMAL_PKD is 5
   MINIMAL_PKD[]                       5.2                                        // MINIMAL_PKD for all targets is 5.2
   MINIMAL_PKD[3]                     5.5                                        // MINIMAL_PKD for target 3 is 5.5
   [Growing]MINIMAL_PKD[3]      5.8                                       // MINIMAL_PKD for target 3 in growing mode is 5.5   [Growing][4]MINIMAL_PKD[3] 6.0                                       // MINIMAL_PKD for target 3 in a 4 targets design in growing mode is 5.5

  Latest key words will override previous key words. INCLUDE keyword will guide the program to load another parameter file. Predefined parameters($VariableName$) will replace the corresponding string to the redefined string in all parameters inclulding these inherited from other parameter file. 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([Condition]) only take effect when the program executes the certain function or certain mode in the bracket on the left and/or for certain target in the bracket on the right. Attention: Predefine and Conditional parameters are just supported by Build module.

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  cavity.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 V3 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. DISCARD previous seed library. It will also OVERWRITE previous result file.
    Daemon: Daemon design mode, auto resume from faults. DISCARD previous seed library. It will OVERWRITE previous result file.
    Continue: Standard continue mode. Load previous seed library. It will APPEND to previous result file.
    DContinue:Daemon continue mode, auto resume from faults. Load 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
    Score: Estimate the ligand binding affinity of results by Score function
    Recommend: Help user to select top elites from large result sets.
    Cluster: Clustering results
    ReportCls: Report the clustering results in HTML
    Synthesize: Perform synthesis analysis
    ReportSyn: Report the synthesis analysis results in HTML

    Tools:
    Seed: (a) Extract seed structures from known inhibitors( for growing and linking strategies) (b) Mapping and pairwise user's seed files in multi-target design mode
    Interaction: Extract key interactions from known inhibitors to construct target-specific biased scoreing function
    Derivation: Hetro-ring replacing
    Search: Substructure searching
    Similarity: Similarity searching

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

5. Example for using LigBuilder V3

    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                                       // set the receptor path to target PDB file
            -----------------------------------------------------------------
            RECEPTOR_FILE                          receptor/1db4.pdb
            -----------------------------------------------------------------

    3) Run Cavity:

            ./cavity     cavity.input

    4) Determine cavity id of target binding site and estimate the ligandgability (it is better to visually check):

            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                                         // set the receptor info based on result 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-just-example.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 (eg. run_1db4.list) to a computer cluster rather than run them sequentially in practice.The tasks in the list file will not automatically run, user should run them by yourself.
            2: It is not necessary to make all tasks run or finished. User can even carry out tasks on different operation systems and then copy the output files to the outputting path assigned in the "LigBuilderV3/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 connection 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 more than one server for one design task.

NOTICE: the build-just-example.input is just for a quick show, user should use the LigBuilderV3/build/build.input as templates of parameters of real projects. The LigBuilderV3/build is also the working directory of LigBuilder, and all operation should be execute in the directory

    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.