Search for oligopeptide fragments
pip install pysuper==0.2.91
Super is able to rapidly search of 3D structural databases. Given a query fragment, Super searches through a database of 3D structures for the query within a tolerence threshold (measured by RMSD).
There are a few dependencies required to build and run Super:
./configure --prefix=${HOME}/some/install/path
I say ${HOME} so that I don't have to install as superuser. I often use --prefix=${HOME}/install
make && make install
in ${prefix}/bin directory: $ LD_LIBRARY_PATH=../lib ./super [OPTIONS...] ${pdb_path}/pdb.db
Options listing from ./super --help:
Usage: super [OPTION...] DATABASE
super -- A 3D protein pattern search program.
-c, --thread-count=COUNT Concurrently process the database with COUNT
threads of control
-d, --defaults Keep default arguments.
-g, --disable-gershgorin Disable use of gershgorin circles for Jacobi
diagonalisation
-l, --lowerbounds=BOUNDS Comma separated list of lower bound checks to use
-n, --disable-rmsd Disable the full (Kearsley) RMSD calculation, just
use the LB
-o, --output=OUTPUT Output to OUTPUT instead of stdout
--quiet Produce no output
-q, --query=QUERY Query database
-r, --disable-mmap Disable use of memory mapped databases to speed up
calculations
-t, --threshold=THRESHOLD Pattern matching threshold measured in Angstrom
-?, --help Give this help list
--usage Give a short usage message
-V, --version Print program version
Mandatory or optional arguments to long options are also mandatory or optional
for any corresponding short options.
I usually run with:
LD_LIBRARY_PATH=${HOME}/install/lib ./super --lowerbounds=arithmetic --threshold=1.0 --query=qry.db pdb.db
OR ON Mac OSX:
DYLD_LIBRARY_PATH=${HOME}/install/lib ./super -t 1.0 -q qry.db pdb.db
An up-to-date pre-processed version of the entire PDB is available for download from http://lcb.infotech.monash.edu.au/super/pdb.db
To generate a query:
python pdb_pp.py --query [YOUR PDB FRAGMENT FILE].pdb --output myquery.qry
To generate a searchable database from a directory containing PDB files (pdb/):
python pdb_pp.py -o pdb.db pdb/