MoMA-LigPath is an application built on our software platform Molecular Motion Algorithms (MoMA). Starting from the model of a protein-ligand complex, MoMA-LigPath computes the ligand exit path from the active site to the protein surface using robotics-inspired algorithms.
In the current version, flexibility is considered for the ligand and all the protein side-chains, and only geometric constraints are taken into account. Flexible protein backbone and energies will be introduced in subsequent versions. Note that cyclic ligands are not accurately treated yet (i.e. cycles are assumed to be rigid). The PDB file provided as input may contain several ligands. Note however that, in the current version, only one ligand (the last ligand in the file) is considered to be mobile. Note also that the input PDB file requires some cleaning up and formatting. This is automatically done in a pre-processing stage performed by the web server. Nevertheless, manual cleaning/formatting following the instructions provided in the Help page is preferred in order to avoid possible mistakes.
Accessing as an anonymous user is possible. Nevertheless, we recommend frequent users to create an account, to have access to a record of the jobs they submit to the server, and to be informed about results by email.
Before submitting your first job to the server, please go to the Demo page, where you will find explanations on how to use the server. Complementary information and answers to frequent questions can be found in the Help page.
You can Contact us for any question about MoMA-LigPath. If needed for intensive use, binaries (Linux or MacOS) of the application can be provided on demand.
Please cite (at least) one of the publications listed in the References page if you use results provided by MoMA-LigPath in your work.
Data and results of each user will not be accessible to other users. However, we cannot guarantee full privacy, and we assume that data submitted to the server are not strictly confidential.