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I-TASSER-MR is a pipeline of automated molecular replacement (MR), designed for solving the phase problem of distant-homology proteins in X-ray crystallography. Starting from the amino acid sequences, 3D models are constructed by I-TASSER based structural assembly simulations, where the unreliably modeled regions with high variation are truncated by a progressive edit procedure. Multiple seed models with different truncations are then submitted to MR-REX, for molecular replacement search by replica-exchange Monte Carlo simulations. For each I-TASSER model, up to 60 copies of truncated models are attempted and the top five solutions ranked by the free R factor of the CNS refined models are returned.

An illustrative example of the I-TASSER-MR output can be found here. For each target, the output data are kept online for three months before they are removed from the server.

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I-TASSER-MR online server

Copy and paste your sequence here (<1,000 residues, in FASTA format and click here for an example. It will take ~16 hours for the example to run through all the steps of I-TASSER-MR):

Or upload the sequence from your local computer:   
Reflection File (mandatory, mtz format, click here for the example mtz file):


Copy Number (mandatory, the number of molecules in the asymmetric unit, should be a number between 1 and 8):

B-factor Selection Constant (Default)   ACC based (accessible surface-area based)   AVS based (average variation score based)  

I-TASSER Model Selection Top 1 model (Default)
Top 5 models (Up to 5 I-TASSER models will be used for MR, which may take a longer time.)

ID (optional, your given name of the protein):

Email (optional, where results will be sent to):



References:

  • Y. Wang, J. Virtanen, Z. Xue, Y. Zhang. I-TASSER-MR: automated molecular replacement for proteins without close homologs using iterative fragment assembly and progressive sequence truncation, Nucleic Acids Research, accepted (2017).
  • Y. Wang, J. Virtanen, Z. Xue, J. J. G. Tesmer and Y. Zhang. Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. Acta Cryst. (2016). D72, 616-628 [PDF] [Support Information] [Source code I-TASSER-MR.tar.gz]


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