SERVER FOR COMPUTING/PREDICTING DEPTH, CAVITY SIZES, LIGAND BNDING SITES AND pKa
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 )
(see doc/documentation or QUICK_START for documentation)
(BLAST and UniRef sequence database downloads are provided at the end of the page)
- tar -xvf depth-2.0.tar.gz
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 (superceded by DEPTH-2.0.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)
syntax: (see doc/ for documentation)
- tar -xvf depth-1.0.tar.gz
- cd depth-1.0
- make or make install
|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)
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-2.2.22 used in the server can be downloaded here.
Alternatively, a copy can be obtained from NCBI FTP site.
Reduce is an external software from Richardson Laboratory that is used in pKa prediction
It can be obtained from here.