mTM-align

Introduction

mTM-align is a server for for efficient protein structure comparisons, which includes are two related modules. The first is for fast database search with one input structure. The second is for multiple structure alignment with two or more input structures. For the first module, it takes about 2-5 minutes for a structure of a medium size (~300 residues). After the search is done, a multiple structure alignment is performed automatically with the top 10 structure, using the second module. The users are also able to select other structures from the returned list to perform multiple structure alignment. For the second module, it takes a few seconds for input of ~10 structures of medium size.



Warning: the server is under maintenance due to an unexpected hardware issue.
For multiple protein structure alignment, please download the package to run locally.

Submit

  • Provide the protein structure (mandatory, uploaded structure should contain only a single chain/model.)  
    •

    Please copy and paste your structure below (in PDB format or in mmCIF format). Click here for an example PDB input...   Click here for an example mmCIF input...

    Or upload the structure file in PDB format or mmCIF format.

    Or provide the PDB id and chain or a SCOPe id.  Click here for an example PDB ID...  Click here for an example SCOPe ID...

  • Other information (optional)
    • > Select database (version 2019-08-04): (optional, the default is Chain)
     Chain (~468k chains)     Domain (~727k domains)     Auto

    > Split structure into domains: (optional, the default is 'No'. You can select "yes" to split your structure into domains automatically, but it may be inaccurate sometimes).
     No     Yes

    > Email: (Optional, where the results will be sent to)

    > ID: (Optional, your given name to this structure. The default is 'query')

    Keep my results private (check this box if you want to keep your job private. A key will be assigned for you to access the results)


    The server is under maintenance due to an unexpected hardware issue.

  • Provide the protein structures (mandatory, uploaded structures should contain only a single chain/model.)  
    •

    Please put all of your structures (in PDB format or in mmCIF format) in a folder, compress it first, and then upload it below.
    (acceptable tarball includes *.tar, *.tar.bz2, *tar.gz, *.tar.xz, *.tgz, *.xz and *.zip format). Click here to download an example PDB input...     Click here to download an example mmCIF input...

  • Other information (optional)

    • Email: (Optional, where the results will be sent to)

    ID: (Optional, your given name to this protein family. The default is 'your_protein')

    Keep my results private (check this box if you want to keep your job private. A key will be assigned for you to access the results)


    The server is under maintenance due to an unexpected hardware issue.
    Please provide all of your structure PDB ID and chain.  Click here for an example input...
    Index PDB ID, Chain
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  • Other information (optional)

    • Email: (Optional, where the results will be sent to)

    ID: (Optional, your given name to this protein family. The default is 'your_protein')

    Keep my results private (check this box if you want to keep your job private. A key will be assigned for you to access the results)


    Please provide all of your structure SCOPe ID and chain.  Click here for an example input...
    Index SCOPe ID
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  • Other information (optional)

    • Email: (Optional, where the results will be sent to)

    ID: (Optional, your given name to this protein family. The default is 'your_protein')

    Keep my results private (check this box if you want to keep your job private. A key will be assigned for you to access the results)


    Please upload all of your structure file in PDB format.
    Index Upload Your Own Structure File
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  • Other information (optional)

    • Email: (Optional, where the results will be sent to)

    ID: (Optional, your given name to this protein family. The default is 'your_protein')

    Keep my results private (check this box if you want to keep your job private. A key will be assigned for you to access the results)


    Please upload all of your structure file in mmCIF format.
    Index Upload Your Own Structure File
    1.
    2.
    3.
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    5.
    6.
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    8.
    9.
    10.
  • Other information (optional)

    • Email: (Optional, where the results will be sent to)

    ID: (Optional, your given name to this protein family. The default is 'your_protein')

    Keep my results private (check this box if you want to keep your job private. A key will be assigned for you to access the results)


    References

  • R Dong, S Pan, Z Peng, Y Zhang, J Yang, mTM-align: a server for fast protein structure database search and multiple protein structure alignment, Nucleic Acids Research, 46: W380-W386 (2018).
  • R Dong, Z Peng, Y Zhang, J Yang, mTM-align: an algorithm for fast and accurate multiple protein structure alignment, Bioinformatics, 34: 1719-1725 (2018).