ANMPathway


ANMPathway

Find transition pathway between two protein conformations


Tutorial

ANMPathway provides an efficient computational method that generates an energetically favorable pathway between a pair of stable states. The algorithm searches for the structure with highest energy that the system is most likely to visit during the transition and created two paths starting from this structure and proceeding toward the end states. Here, we will use an example to demonstrate how to use our web interface.

STEP 1

We will use open and closed state of adenylate kinase structures, PDB:4AKE and PDB:1AKE, respectively, for our example.

STEP 2

Adenylate kinase is monomeric protein, however, these PDB files contain two copies of the monomeric units. Thus, chain B is deselcted. We will use default parameters for the calculation.

STEP 3

Because some calculations can take long time, we use queueing system for the calculation. You can use the link provided to monitor the status of your job. Notification e-mails will be sent to the provided e-mail address when the job is submitted, started, and finished.

STEP 4

When the calculation is done, a set of output files are delievered to the e-mail address provided. These output files are: