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PredZinc version 1.4, 2011-10-14
PredZinc is a program for predicting zinc-binding sites in proteins from their
amino acid sequences. The program is witten in c/c++ and bash shell scripts.
Currently, PredZinc can be run on Linux and Windows (with Cygwin).
PredZinc is copyrighted (c) to Nanjiang Shu, Structural Chemistry, Stockholm
University, Sweden and is free for academic use.
****************************************
The webserver of PredZinc is available at
http://casio.fos.su.se/server/predzinc
****************************************
Reference:
Nanjiang Shu, Tuping Zhou and Sven Hovmoller (2008). "Prediction of
zinc-binding sites in proteins from sequence." Bioinformatics 24(6):
775-782.
================================================================================
usage: predzinc.sh [-cpu INT] [-outpath DIR] [-blastdb STR] [-db STR]
[-pssm FILE] [-pssmfilelist LISTFILE]
[-showexample] [-verbose] [-version] [-not-clean] [-h]
[-outname STR]
FILE
Note: The supplied sequence FILE should be in Fasta format
Do not use ';' in the rootname of the input file
since it will be used as field separator.
Options:
-cpu INT Set the number of cpu cores to be used to run
PSI-BLAST, (default: 1)
-outpath DIR Output the result to the specified path, (default: ./)
-outname STR Output name, (default: query)
-blastdb FILE Database for psi-blast, (default: $BLASTDB/nr)
-db STR Database for PredZinc, (default: passe)
-pssm FILE Supply pssm file in PSI-BLAST -Q flag output format,
if supplied, PSI-BLAST will not run
-pssmfilelist FILE Supply a file with a list of pssm files for batch mode
prediction
-not-clean If supplied, the temporary files will be kept
-verbose Print verbose information
-version Print version
-showexample Print How to use with examples
-h|--help Print this help message and exit
Note that the rootname of the file should be <= 100 characters.
Examples:
# In the subfolder "test"
# Carry out the prediction by supplying sequence file (with one or more
# sequences) in Fasta format
../predzinc.sh test3seq.fa
# Carry out the prediction by supplying a single pssm file
../predzinc.sh --pssm 2AZ4A.pssm
# Carry out the prediction by supplying a list of pssm files
../predzinc.sh --pssmfilelist test.pssmfilelist
================================================================================
DOWNLOAD:
http://www.fos.su.se/~nanjiang/zincpred/download/
http://casio.fos.su.se/server/predzinc/download/predzinc.tar.gz
================================================================================
INSTALLATION:
download the package
for Linux : predzinc_linux.tar.gz
for Windows (Cygwin) : predzinc_cygwin.tar.gz
then untar the file by
tar -xvzf predzinc_linux.tar.gz
or
tar -xvzf predzinc_cygwin.tar.gz
Go to the uncompressed folder "predzinc" and run
make
make install
Make sure that NCBI nr database formatted for PSI-BLAST is installed. The
environmental variable BLASTDB points to the directory storing nr blast
database needed by PSI-BLAST
export BLASTDB=path-storing-blast-nr-database
e.g.
export BLASTDB=/data/blastdb
If your operating system is x86 linux or cygwin, you should be able to run the
program by the pre-compiled executables already
Test running: go in to the subfolder "test" and run
../predzinc.sh 2AZ4A.aa
================================================================================
Others:
The blastpgp used in this version of PredZinc is 2.2.25.
If you want to use a different version of PSIBLAST, please copy the program
'blastpgp' to $PredZinc/bin and the corresponding matrix file to $PredZinc/data
cp blastpgp $PredZinc/bin
cp BLOSUM62 $PredZinc/data
The gist-svm used in this version of PredZinc is 2.1.1
If you want to use a different version of gist-svm, please copy the program
'gist-svm-train', 'gist-classify' and 'gist-score-svm' to $PredZinc/bin
cp gist-svm-train $PredZinc/bin
cp gist-classify $PredZinc/bin
cp gist-score-svm $PredZinc/bin
================================================================================
Running time:
It takes on average about 6 minutes to predict a protein sequence with 300
amino acids, when running on a single core with 2GHZ cpu and 4GB RAM. Most
time is taken by PSI-BLAST for building the sequence profile. When the
sequence profile is obtained, it takes about one minute to get the
prediction result.
================================================================================
Examples:
in the "test" folder, run
../predzinc.sh 2AZ4A.aa
or if the pssm file is already built
../predzinc.sh --pssm 2AZ4A.pssm
The result of the predict will be output to "query.predzinc.report"
as shown below.
Res : three-letter amino acid code
SerialNo : the residue number in sequence, starting from 1
Score the : predicted zinc-binding score for the residue, ranging from 0 to 1
*********** Begin the file query.predzinc.report ***********************
Zinc-binding site prediction by PredZinc version 1.3 (c) Shu.
Reference:
Shu, N., Zhou, T. and Hovmoller, S. (2008) Prediction of zinc-binding
sites in proteins from sequence, Bioinformatics, 24, 775-782.
Parameters:
Training set: 2727 PDB chains
blastpgp version: 2.2.25
blast nr database: 10,083,419 sequences
//BEGIN query 1
Your input amino acid sequence (containing 429 aa) is
MESKAKTTVTFHSGILTIGGTVIEVAYKDAHIFFDFGTEFRPELDLPDDHIETLINNRLVPELKDLYDPR
LGYEYHGAEDKDYQHTAVFLSHAHLDHSRMINYLDPAVPLYTLKETKMILNSLNRKGDFLIPSPFEEKNF
TREMIGLNKNDVIKVGEISVEIVPVDHDAYGASALLIRTPDHFITYTGDLRLHGHNREETLAFCEKAKHT
ELLMMEGVSISFPEREPDPAQIAVVSEEDLVQHLVRLELENPNRQITFNGYPANVERFAKIIEKSPRTVV
LEANMAALLLEVFGIEVRYYYAESGKIPELNPALEIPYDTLLKDKTDYLWQVVNQFDNLQEGSLYIHSDA
QPLGDFDPQYRVFLDLLAKKDITFVRLACSGHAIPEDLDKIIALIEPQVLVPIHTLKPEKLENPYGERIL
PERGEQIVL
The following 5 residues were predicted as zinc-binding for protein "2az4_A" (with score >= 0.450), sorted by scores
Res SerialNo Score
HIS 92 0.878
HIS 94 0.878
HIS 167 0.844
ASP 96 0.669
HIS 404 0.614
Prediction scores for the rest 84 selected residues, sorted by scores
Res SerialNo Score
HIS 382 0.372
GLU 237 0.321
ASP 189 0.245
HIS 97 0.114
HIS 193 0.091
GLU 409 0.029
HIS 182 0.025
ASP 65 0.022
GLU 205 0.019
GLU 216 0.019
GLU 417 0.016
GLU 303 0.016
ASP 166 0.013
HIS 31 0.010
GLU 161 0.007
GLU 296 0.006
ASP 324 0.005
GLU 136 0.005
GLU 199 0.005
GLU 396 0.005
HIS 50 0.004
GLU 39 0.004
ASP 35 0.004
GLU 115 0.004
GLU 422 0.003
GLU 157 0.003
CYS 379 0.003
ASP 389 0.003
HIS 12 0.003
GLU 341 0.002
GLU 282 0.002
GLU 198 0.002
ASP 29 0.002
GLU 62 0.002
ASP 68 0.002
HIS 195 0.001
HIS 347 0.001
GLU 238 0.001
GLU 309 0.001
GLU 52 0.001
HIS 85 0.001
GLU 224 0.001
ASP 45 0.001
GLU 425 0.001
GLU 273 0.001
GLU 74 0.001
GLU 24 0.001
ASP 49 0.001
GLU 137 0.001
GLU 226 0.001
ASP 371 0.000
ASP 105 0.000
ASP 168 0.000
GLU 291 0.000
ASP 349 0.000
GLU 211 0.000
ASP 128 0.000
GLU 315 0.000
GLU 250 0.000
GLU 248 0.000
GLU 143 0.000
GLU 386 0.000
HIS 76 0.000
HIS 209 0.000
CYS 204 0.000
ASP 357 0.000
ASP 355 0.000
ASP 48 0.000
GLU 266 0.000
HIS 243 0.000
ASP 387 0.000
ASP 337 0.000
ASP 319 0.000
ASP 181 0.000
GLU 79 0.000
GLU 43 0.000
ASP 80 0.000
GLU 412 0.000
ASP 82 0.000
ASP 151 0.000
ASP 239 0.000
GLU 2 0.000
ASP 228 0.000
ASP 365 0.000
//End