MoMA LigPath

Advanced Mode Demo

Please follow the steps below to submit a job to MoMA-LigPath.

Step 0 : amc generation

Before submitting a job as advanced user, you have to create an .amc file describing the flexibility of molecules.
Using the "AMC file generator", you can create a template .amc file from a .pdb file. Then, you can modify the file using any text editor.
Please go to the Help page for more information about the .amc file format. You will also find explanations in the header of the .amc template file.

Step 1 : job name

Give a name to your job. It will be its identifier in your job list.
This is not required for anonymous users.

Step 2 : upload files

Step 3 : parameters

You can optionally tune parameters :
  • Basic parameters :
    • % of van der Waals radii : 75 % is a reasonable default value. A lower percentage may be necessary to find solutions to very constrained problems, which would require some flexibility of the protein backbone. In easy cases, you can increase this percentage, thus forcing the ligand to move along the medial axis of the access/exit pathway.
    • Number of paths : you can obtain more than one solution for each job. For each solution path, you will obtain a sequence of .pdb files.
  • Advanced parameters :
    • RRT expansion strategy : By default, MoMA-LigPath applies an RRT-Connect strategy for the expansion of nodes. You can change this for a more basic RRT-Extend strategy, which generally produces shorter local paths, thus being more computationally expensive. Please refer to basic literature on the RRT algorithm for further explanations on these strategies.
    • Exit distance : You can specify here the length of the paths to be computed by MoMA-LigPath by defining the distance (in angstroms) that has to be reached between the geometric centers of the ligand and the protein. When left unspecified, the exit distance is automatically computed by MoMA-LigPath, based on the molecule sizes.
    • N fail max : This parameter determines the number of consecutive expansion failures after which a node is considered to be an "exhausted node", and is no more selected for expansion during the RRT construction. The default value, 50, provides good results in general. This value can be increased for very constrained problems.

Step 4 : submit job

Once the steps above have been completed, you can click on the "Submit" button.
If all inputs are correct, your job will be pushed in the stack of jobs to be treated by the server.
If you are a registered user, you will receive an email when your job will be treated. Then, you will have access to the results by clicking on the My jobs item of the menu.
As an anonymous user, you will be redirected to a webpage having a unique URL. Please bookmark this URL for a subsequent access to get results. Note that the time required to treat your job may be long, depending on the workload of the server.

Results

Each job correctly submitted to MoMA-LigPath generates a folder containing input data and results that you can download. The image below illustrates a job that was successfully solved, and for which a single path was requested.
The main output of MoMA-LigPath is a sequence of .pdb files corresponding to intermediate conformations of the molecules along the ligand exit path. In addition, an Execution Report provides information about parameters used and operations performed by the program. If no solution is found, the Execution Report provides indications on possible causes of failure.
In addition to downloadable files, the solution path can be directly visualized on the Web by means of a Jmol applet. Here you can see the solution for the sample1 problem used in this demo. Note that the applet has to download a large amount of data, which may require significant time depending on the speed of your internet connection.
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Next demo page : Simple mode