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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 structure search could be performed on different databases include PDB, SCOPe, CATH, BFVD, and AlphaFoldDB. The multiple protein structure alignment is performed using the fast and accurate algorithm mTM-align.


The database search consists of two steps:

  • Computing the cosine similarity of the query's feature with the targets' features. Targets with high cosine similarity are considered to be the candidates for high-speed retrieval.
  • For high-accuracy retrieval, the candidates from high-speed retrieval are further filtered using fTM-align. Results with TM-score higher than 0.4 are returned.

    • 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).