PROTEUS Structure Prediction Server 2.0
Comprehensive 2D and 3D structure predictions




Problems or questions? Please use our feedback form.


Databases for Installation

Test Data Sets



  • System
    • You need a standard *nix system (Linux, Unix, BSD, Mac OSX 10.4+ (10.4+ because Java 1.5 doesn't run on any lower)). A Linux system is recommended, as the tmhmm binary will not run on a Mac. If you do not want to run transmembrane predictions, you may use a Mac (transmembrane homolog searches will still work).
    • At least 512 MB of RAM is required, but it doesn't work very well with less than 1 GB.
  • Java VM
    • You need Java 1.5 or higher to run PROTEUS2. Download it here.
  • Programs
    • You need BLAST installed. Download it here. PROTEUS2 has been tested with blast 2.2.12.
    • ClustalW is required. Download it here
    • PROTEUS2 will install PSIPRED, JNET, XAlign, tmhmm, tmbhunt, homodeller, and gafolder for you.
      Click to download PROTEUS2 distribution (47M)
  • Databases


  • Make sure you have all the requirements list above (the proteus distribution and the NR database).
  • Uncompress the application.

    linux > unzip
    linux > cd proteus

  • Uncompress the NR database. Remember where you uncompress it to.

    linux > tar xzvf filtnr.tar.gz

  • Run the setup application.

    linux > sh run_setup
    Welcome to the PROTEUS2 Setup Program!

  • Answer all the questions. It *should* do the rest, including running a few diagnostics. If there are any problems, see the troubleshooting section below. Otherwise, email me.
  • To run a prediction, run
    linux > sh run_proteus <filename>

    The input file can be in FASTA format or in raw sequence format. PROTEUS2 will figure it out.
  • For additional options, see
    linux > sh run_proteus --help

  • For an example file, check "test/test1.fa"

    linux > sh run_proteus test/test1.fa


  • If you see a weird message like: Exception in "main": UnsupportedClassVersionError: Unsupported major.minor version (49.0) the reason for this is that Java 1.5 is not being run. The "run_setup" command assumes that running "java" is running java 1.5. Type "java -version" to make sure this is running java 1.5. If it isn't, change "java" to point to java 1.5.
  • If something in the setup goes wrong, you can try compiling the dependencies yourself:
    cd <proteus_dir> src/jnet/src/
    cd <proteus_dir> src/psipred/src/
    cd <proteus_dir> src/xalign/
  • When setup completes, it should write all your values to an XML file called "proteus.config" in the root proteus2 directory. Check that these values are correct.
  • If you haven't setup BLAST to run before, there are a few things you need to know to get it working.
    The setup program should try running BLAST as part of the setup process. If it fails, try running it from the command line (in the proteus2 root directory):

    blastpgp -m6 -a 1 -b750 -e 0.01 -j 3 -h 0.001 -Q test.pos -d <path to DB> -i test/test1.fa -C test.chk

    This should produce a result. If it doesn't there are a couple of things that can go wrong.
    • You need a ".ncbirc" file in your home directory, with the content:
      Data=<path to BLAST>/data
    • OR set the BLASTMAT environment variable to "<path to BLAST>/data"