Please note: Under construction ... coming soon

What's this page for? This page discusses the four-pronged procedure of iSPOT modeling. The docking guides you through computational docking of two proteins (A and B), either by rigid-body or flexible advanced molecular dynamics; and the scattering page provides a near-complete list of tips for exeperimental scattering (aka SAXS); and the footprinting page allows you to upload experimental footprinting rates for protection factor analysis; and collectively, the integration page allows you to select specific parameters for the iSPOT-determined structures; Finally, the tutorial guides you through a basic example.




1. Computational protein-protein docking

What is computional protein-protein docking? The iSPOT method was developed to .

Under construction - stay tuned!

Input


The input to docking is the PDB files of two proteins (A and B). Only the ATOM fields of a standard PDB file are recognized.

Select A:
Select B:

Post-docking clustering matrix:  
 oRMSD -- accounting for mutual orientation of A and B
 fRMSD -- a regular RMSD for the entire complex

Choose the appropriate RMSD value:
    

         

Output


The output of docking is a series of protein models. A set of top conformations is available for download if needed.








 Email Notification [optional]  Your email address will be used to notify you upon completion of the job. If left empty, you'll have to manually refresh your working directory to assess the job's completion, and bookmark it so that you can get to it at a later time.

    Email: 




2. Small-angle X-ray scattering (SAXS)


What is small-angle X-ray scattering (SAXS)? In short, shape information and specically, protein arrangments can be inferred from SAXS data. A berif overview of SAXS can be found at

Methods for SAXS-based Structure Determination of Biomolecular Complexes
Advanced Materials 26 7902–7910 (2014) Sichun Yang

The Fast-SAXS-pro software is used for SAXS computing as a method of choice. Please refer details at

Fast-SAXS-pro: A unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexes
Journal of Chemical Physiscs 138 (2) 024112 (2013) Krishna M Ravikumar, Wei Huang and Sichun Yang

Upload SAXS data

The input is the experimental scattering data . A three-columb data file is needed (q, I, and s.d.) .





         


Tips for data collection

For developers, the pa.




3. Hydroxyl radical footprinting


What is hydroxyl radical footprinting? It is a labeling technique. Instead of using any isotopes, it uses X-rays to generate hydroxyl radicals from water that react (or label) the proteins. More detaisl can be found at

Quantitative mapping of protein structure by hydroxyl radical footprinting mediated structural mass spectrometry: A protection factor analysis
Biophysical Journal 108 (1) 107–115 (2015) Wei Huang, Krishna M Ravikumar, Mark Chance, and Sichun Yang

Uploading FP rates

The input is the experimental footprinting data . A two-columb data file is needed (residue vs rate) .





         

Tips

For developers, the pa.




4. Intergation by iSPOT


What is the integration and optimization? The iSPOT method was developed to ... . More details can be found at

Theoretical modeling of multiprotein complexes by iSPOT: Integration of small-angle X-ray scattering, hydroxyl radical footprinting, and computational docking
Journal of Structural Biology 196 (3) 340-349 (2016) Wei Huang, Krishna M Ravikumar, Marc Parisien, and Sichun Yang

Paraemters:



    Two-dimensional scoring matrix:  

     scattering-based scoring
     footprinting-base scoring
     both




Under construction - stay tuned!

Input


Please choose a protein 3D structure to dock against a nucleic acid.
Maximum 500 residues. Only the ATOM fields of the PDB file are recognized.

    

         


The input to a A analysis is a series of of the same .... presence of different ligands.

Output

The output of a analysis is a series of protein models conformations.

 Email Notification [optional] 
Please provide your email address so that the web server can notify you upon completion of the job. This field is optional. If left empty, you'll have to manually refresh your working directory to assess the job's completion, and bookmark it so that you can get to it at a later time.

    Email: 


Contact

Email:  sxy

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