In this example, L-RIP and RIPlig simulations of HSP90 will be analysed.


1. Overview:

The heat-shock protein HSP90 is a potential target for the treatment of cancer by inhibition of its ATPase activity. The ADP binding pocket contacts an unstable alpha-helix that undergoes distortion in the middle, converting into two short helices connected by a loop inbetween. (PDB structure: 1UYD ; Reference ligand: ADP)

In this example, two sets of trajectories are simulated by using the L-RIP and RIPlig methods. These methods can be done simultaneously (as shown in this example) or separately. Then the simulated trajectories are analyzed using TRAPP-analysis and TRAPP-pocket.

2. To run these examples, you need the following files and parameters:

  • 1UYD_protein.pdb
  • Protein PDB structure (extracted by "grep ATOM 1UYD.pdb > 1UYD_protein.pdb" from the co-crystallized structure)


  • 1UYD_ligand.pdb
  • Ligand PDB structure (extracted by "grep HET 1UYD.pdb > 1UYD_tmp.pdb; grep -v HOH > 1UYD_ligand.pdb" from the same structure)


3. Simulation procedure and results:




Fig.1: Three different crystal structures co-crystallized with ligands are illustrated in the figure. The structures 3bm9, 1byq, and 1uyd along with the corresponding ligands BXZ (3bm9), ADP (1byq), and PU8 (1uyd) are shown in blue, red, and gray respectively. For more details see here.

Simulation procedure and results: RIPlig

  • Step 1: Uploading input data
  • Upload the reference protein and ligand structures (1UYD_protein.pdb and 1UYD_ligand.pdb), choose RIPlig methods for simulation, give the number of RIPlig snapshots to be stored (100 is chosen in the present example).




Fig.2: Your webpage will look like this.


Simulation procedure and results: L-RIP

  • Step 1: Uploading input data
  • You have to upload the reference protein and ligand structures (1UYD_protein.pdb and 1UYD_ligand.pdb), choose L-RIP method for simulation, and the number of L-RIP snapshots to be stored (100 is chosen in this example).




Fig.3: Your webpage will look like this.


  • Step 2:Preview and Starting simulations
  • On the next page Pocket analysis will be started with the following parameters you must be able to see the JSmol visualization of the reference structure, a ligand, as well as identification of the binding pocket.




Fig.4: Your webpage will look like this.


  • Step 3: View results of TRAPP-structure and TRAPP-analysis
  • Use the link View Analysis and View cluster representatives in JSmol


Fig.5: RSMD plots (Note the residue numbering has changed from the original input as described on the summary input and residue mapping page).



Fig.6: Cluster representation




Fig.7: Clusters along the trajectory.


  • Step 4: Re-run TRAPP-analysis using k-means clustering with additional residues.
  • For this you have to use the button Re-run TRAPP-analysis. We added additional residues so that the complete list of binding site residues is: A:33 A:34 A:36 A:37 A:38 A:39 A:40 A:78 A:79 A:80 A:81 A:82 A:83 A:84 A:85 A:86 A:87 A:88 A:89 A:90 A:91 A:92 A:93 A:94 A:95 A:96 A:97 A:98 A:99 A:100 A:101 A:102 A:103 A:104 A:105 A:120 A:121 A:122 A:123 A:124 A:135 A:147 A:169.




Fig.8: Your webpage will look like this.



Fig.9: RMSD Results



Fig.10: JSmol Representation



Fig.11: Cluster Representation



Fig.12: Clusters along the trajectory.


  • Step 5: Run TRAPP-pocket
  • Click on the button Run TRAPP-pocket.




Fig.13: Your webpage will look like this