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About the server

The server consists of two related modules: fast search of structure database and multiple protein structure alignment. The database search is speeded up based on a heuristic algorithm and a hierarchical organization the structures in the database. The multiple protein structure alignment is performed using the fast and accurate algorithm mTM-align.


The database search consists of three steps:

  • To speed up the database search, the sequence of the query structure is first searched by PSI-BLAST against a non-redundant structure domain database DOM50 (contains about 40,000 structures with pairwise sequence identity <50%). If hits with e-value <0.001 are found, an iterative method (named Walk) (that considers the pairwise TM-score of the structures in DOM50) will be used to expand these hits to more structures in DOM50. If no hits are found by PSI-BLAST, the query structure will be compared against the DOM50 database using fTM-align (a fast version of TM-align), which is 5-10 times faster than TM-align and with similar accuracy.
  • The top 200 templates from DOM50 are then expanded to the whole domain database (with about 500,000 structures), to find all templates with TM-score>0.5 to the query structure.
  • An automated multiple structure alignment is then performed using the top 10 templates. The users are also able to select other templates for making multiple structure alignment.

    • The multiple structure alignment is built with three steps:

  • Generating all the Pairwise structure alignments for the input structures with TM-align.
  • A structure-based phylogenetic tree is constructed using the UPGMA algorithm.
  • Progressive construction of a multiple protein structure alignment using the branching order from the phylogenetic tree.


    • Figure 1. The flowchart of mTM-align server.




    Figure 2. The navigation bar of mTM-align server.




    Figure 3. The submssion page of Fast Search of Structure Database.



    Input of Multiple Protein Structure Alignment


    Figure 4. The submssion page of Multiple Protein Structure Alignment.




    Figure 5. The output of Fast Search of Structure Database.



    Output of Multiple Protein Structure Alignment


    Figure 6. The output of Multiple Protein Structure Alignment.



    Reference

  • 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).