PROSPECT Version 2.0: Introduction Installation Quick Guide Running Prospect Manager Input Formats Templates Parameters Configurations Outputs References FAQ

Computer Requirement PROSPECT can basically run on any platform with the Unix or Linux operating system and a C compiler. It has been tested on Silicon Graphics, Sun, DEC, MacOSX, and Linux PC (Not all of these are included in the distribution, if you need prospect for another UNIX platform, let us know). A large memory, preferably >256Mb, may be needed for threading of big proteins. A large cache size can significantly accelerate the computing speed. Installation Please use the following steps to install PROSPECT: Decompress and untar the prospect.tar.gz file, this should leave a directory called prospect Edit your shell script to set PROSPECT_PATH to the location of the direcory where prospect is located (it contains the data and bin folders) If you want to be able to produce 3D models, download the subset of PDB used as templates if you do not have a local copy of PDB. Enviromental varibles to set These are the eviromental that must be set in order to allow prospect to run correctly. If you are using a C shell, the command would be something like setenv PROSPECT_PATH /usr/local/prospect If you are using BASH, the command would be something like: export PROSPECT_PATH=/usr/local/prospect Basic Run: PROSPECT_PATH Prospect uses this variable to find it's tools and databases.  Should be set to the path of the directory that contains the bin and data directories. This enviromental varible is required by all prospect tools. BLASTPGP_EXE Points to the blastpgp application.  Required for template creation and running the get_chk_file script. BLASTPGP_DB Points to the protein sequences database used for creating sequence profiles, typically the NR database from NCBI.  Required for template creation and running the get_chk_file script. PVM_ARCH Describes the computer architecture.  Typical definitions include LINUX, LINUXPPC, SUN4SOL, DARWIN, ALPHA. Required for the prospect_manager.pl script. 3D Protein Structure Creation: PDB_PATH Points to the directory that contains source PDB files. MODELLER_EXE Points to the run script of the modeller application RASMOL_EXE Path to the PDB viewer Template Creation: MAKEMAT_EXE Makemat is part of the NCBI toolkit, typicaly in the same directory as blastpgp. DSSP_EXE The secondary structure definition program. Other Tools libxml2 (Required) In order for prospect to work correctly you will need to make sure that libxml2 is installed.  This should be already done in most modern Unixes.  If not, visit http://www.libxml.org download and install the software. BlastPGP (Required) You can find the source and executables for BlastPGP at ftp://ftp.ncbi.nih.gov/blast/ The NR database can be downloaded at ftp://ftp.ncbi.nih.gov/blast/db/nr.Z Perl (Optional various scripts) This should be a standard part of most modern Unix systems Perl/Tk (Optional for GUI interface) The script prospect_modeller.pl uses Perl/Tk to create the GUI interface.  You can find it at http://www.perltk.org/ Rasmol (Optional for viewing 3D structures) You can get a copy at http://www.openrasmol.org/ modeller (Optional for creating 3D structure) Prospect is simply an alignment program.  In order to produce actual 3D models, you will need a copy of the software 'Modeller' found at http://guitar.rockefeller.edu/modeller/modeller.html Prospect has a conversion tool that will extract prospect alignments to a form that can be used by modeller. dssp (Optional for template creation) DSSP is a program to assign secondary structure classifications to known structures in PDB format.  The make_template uses it to create data needed for the template.  You can find it at http://www.cmbi.kun.nl/gv/dssp/