SERVER FOR COMPUTING/PREDICTING DEPTH, CAVITY SIZES, LIGAND BNDING SITES AND pKa


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DEPTH Computation and Binding Cavity Prediction

DEPTH-2.0 is released under LGPL3 license.

  • source code: depth-2.0.tar.gz
  • source code: depth-2.0_noopenmp.tar.gz (without openmp )
  • Instruction:
    • tar -xvf depth-2.0.tar.gz
  • (see doc/documentation or QUICK_START for documentation)
  • (BLAST and UniRef sequence database downloads are provided at the end of the page)

  • DEPTH-1.0 is released under LGPL3 license. (superceded by DEPTH-2.0. See section above)

  • source code: depth-1.0.tar.gz
  • source code: depth-1.0_noopenmp.tar.gz (without openmp)
  • installation:
    • tar -xvf depth-1.0.tar.gz
    • cd depth-1.0
    • make or make install
  • syntax: (see doc/ for documentation)


  • Known bugs
    There has been reported case where the program does not work correctly with the following specifications:
  • iMac with Mac OS X 10.6.8; gcc version 4.2.1 (Apple Inc. build 5666) (dot 3)
  • MacBook Pro with Mac OS X 10.6.8; gcc version 4.2.1 (Apple Inc. build 5664)
  • Sequence Database

    UniRef90 database used in the server can be downloaded here (warning: file size ~3GB).

    Alternatively, a copy can be obtained from UniProt Download Center.

    BLAST download

    BLAST-2.2.22 used in the server can be downloaded here.

    Alternatively, a copy can be obtained from NCBI FTP site.

    'Reduce' download

    Reduce is an external software from Richardson Laboratory that is used in pKa prediction

    It can be obtained from here.