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LS-align is an algorithm designed for atom-level structural comparison of ligand molecules. The target function of LS-align is a combination of inter-atom distance, atom mass, and chemical bond connections; while the final atom-to-atom alignment is generated by maximizing such target function through an enhanced-greedy based, iterative heuristic search algorithm. LS-align program contains two modules: Rigid-LS-align for rigid-body ligand structure comparison; and Flexi-LS-align for flixible structure comparison. In particular, the Flexi-LS-align module seeks for optimal alignments of various alternative conformers of the ligand molecules by rotating flexible bond-angles, which allows the consideration of binding-induced conformational changes in the ligand structural comparison and alignment.

[View an example of output] [Download dataset used in LS-align]

  • Input Query Ligand In MOL2 format (mandatory):
    Please copy and paste your data below. Sample input   

    Or upload the ligand MOL2 file:


  • Input Template Ligand In MOL2 format (mandatory):
    Please copy and paste your data below. Sample input   

    Or upload the ligand MOL2 file:


  • Choose alignment type(s) (You can choose both)
    Rigid alignment (Default)    Flexible alignment

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

LS-align download

  • Click LSalign_src.tar.gz to download the newest version of the source code of LS-align coded in C++. You can compile the program in your Linux computer by:
      >tar zxvf LSalign_src.tar.gz
      >cd src
      >g++ LSalign.cpp -o LSalign
      or
      >g++ -static -O3 -ffast-math -lm -o LSalign LSalign.cpp
  • Click LSalign.tar.gz to download the executable program for Linux and Windows systems. Nevetheless, it is strongly recommended to download the LS-align source code and compile it on your machine, which gives you higher speed to run the program.

LS-align other information

References:
  • Jun Hu, Zi Liu, Dong-Jun Yu, and Yang Zhang. LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening. Bioinformatics, 34: 2209-2218 (2018). [Download download the PDF file] [Support Information]

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