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 web server of PredZinc is available at http://predzinc.bioshu.se
Nanjiang Shu, Tuping Zhou and Sven Hovmoller (2008). "Prediction of zinc-binding sites in proteins from sequence." Bioinformatics 24(6): 775-782. http://www.ncbi.nlm.nih.gov/pubmed/18245129
Nanjiang Shu Science for Life Laboratory, Stockholm
Download the package by
$ git clone https://github.com/nanjiangshu/predzinc
Enter the predzinc directory
$ cd predzinc
Fetch the data set by
$ git lfs fetch
$ git lfs checkout
If you don't have git-lfs installed, please installed follow the instructions at https://git-lfs.github.com/
After that, change to the subfolder predzinc and compile the package by
$ cd predzinc
$ make
$ make install
Make sure that the NCBI uniref90.fasta 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-database
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 predzinc/test
-
Carry out the prediction by supplying sequence file (with one or more sequences) in FASTA format
$ ../predzinc.sh test3seq.fa -outpath out1 -
Carry out the prediction by supplying a single pssm file
$ ../predzinc.sh --pssm 2AZ4A.pssm -outpath out2 -
Carry out the prediction by supplying a list of pssm files
$ ../predzinc.sh --pssmfilelist test.pssmfilelist -outpath out3
##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 30 seconds to get the prediction result. With modern computes, the speed can be significantly faster.
##Result examples:
in the test folder, run
$ ../predzinc.sh 2AZ4A.aa
or if the pssm file is already built, run
$ ../predzinc.sh --pssm 2AZ4A.pssm
The result of the predict will be output to "query.predzinc.report" as shown below. The explanation of the colums in the result file is as follows
*Res : three-letter amino acid code
*SerialNo : the residue number in sequence, starting from 1
*Score : predicted zinc-binding score for the residue, ranging from 0 to 1
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