GalaxyWater-wKGB

Method for GalaxyWater-wKGB

GalaxyWater-wKGB predicts position of water molecules interacting with a protein for a given protein structure by using wKGB statistical potential for protein-water interaction.




Inputs for GalaxyWater-wKGB

User Information

First, you have to enter the following information required for modeling.
  • Job name: Enter job name for your recognition.
  • E-mail address: GalaxyWEB server will send progress reports of your job.

Inputs

You have to provide a protein structure in PDB File Format.





Outputs for GalaxyWater-wKGB

Predicted water positions

Predicted positions of water molecules interacting with the protein are shown.
Three different score-cuts (cut-off values of wKGB potential) can be selected.
More water positions are generated with lower score-cuts.

Download

The provided files include (1) out.pdb that contains all water positions predicted with score cutoff of -2 and
(2) out_scut_x.pdb (x = 6,8,10) that contains water positions predicted with score cutoff of -x.
The value of wKGB potential (multiplied by -1) for each predicted water molecule is written in the B-factor column.



References for GalaxyWater-wKGB
  • L. Heo, S. Park, and C. Seok*, "GalaxyWater-wKGB: Prediction of water positions on protein structure using wKGB statistical potential" (submitted)