GalaxyHomomer

Method for GalaxyHomomer

GalaxyHomomer predicts the protein homo-oligomer structure from its amino-acid sequence or monomer structure.
If the amino-acid sequence is given as input, GalaxyHomomer attempts sequence similarity-based approach,
structure similarity-based approach, and ab initio docking until 5 models are generated. For model 1, automatically detected less reliable loop or terminus regions (called ULR) are re-modeled, and the overall oligomer structure is relaxed using GalaxyRefineComplex. If the monomer structure is given as input, 5 oligomer models are generated by structure similarity-based approach and ab initio docking. If less reliable regions of the input structure are provided by user, these regions are re-modeled during oligomer modeling.
Please note that slightly different results can be obtained in different runs because of the stochastic nature of the optimization algorithm.




Inputs for GalaxyHomomer

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.

GalaxyHomomer Input


You have to provide a protein sequence in the FASTA format
or a protein structure file in the PDB Format for homo-oligomer structure prediction.

Options for assigning oligomeric state


If the oligomeric state of query protein is known or can be predicted, user can provide the oligomeric state.

Options for assigning regions to be refined


User can enter the residue numbers of the loops and termini to be modeled. Please note that this option is available only when user provides the monomer structure as input.


Outputs for GalaxyHomomer

Predicted Structures


The 5 oligomer models are shown in PV. Detected ULRs (less reliable loops/termini) are colored in grey.

Model Information


Oligomer templates, the number of subunits, and interface area are shown. Sequence identity or structure similarity are shown for template-based models while docking score is shown for models predicted by ab initio docking. For each model, detected less reliable regions are provided, and user can run additional refinement including loop modeling and overall structure relaxation by clicking "Submit" button in the table. It is automatically directed to the submit page for additional refinement of the predicted model.

Download

Users can download 5 structures generated by GalaxyHomomer.




Supplementary Information

Response time (sequence input)


Response time depends on the total number of residues in homo-oligomer. If less reliable loop or terminus regions (ULR) are detected for model 1, the job takes more time to refine these regions as shown in above figure (red dots). In most cases, the homo-oligomer structure prediction is finished in 6-12 hours with 16 cores of Intel Xeon E5410 (2.33 GHz).

Response time (structure input)


Response time depends on the total number of residues in homo-oligomer. If only template-based method is used (red dots), the prediction is finished in an hour. In most cases, the homo-oligomer structure prediction is finished in 2 hours with 16 cores of Intel Xeon E5410 (2.33 GHz).




References for GalaxyHomomer