Brief usage notes for MetaPSICOV2
=================================

To run MetaPSICOV2 you need to download and install Blast, PSIPRED, PSICOV,
FreeContact, CCMpred, HHSuite and HMMER separately. Please see relevant home
pages for these packages for information on installation:
http://bioinf.cs.ucl.ac.uk/downloads/psipred
http://bioinf.cs.ucl.ac.uk/downloads/PSICOV
https://rostlab.org/owiki/index.php/FreeContact
https://bitbucket.org/soedinglab/ccmpred
ftp://toolkit.genzentrum.lmu.de/pub/HH-suite

To compile MetaPSICOV, untar, cd to src directory and run "make" followed by
"make install".

A skeleton csh script called run_metapsicov is provided for running all of the
MetaPSICOV steps. Please consult the comments in this script (and the
jackhhblits script) for information on how to customise the installation for
your own setup.

Note: This requires HHBlits 2.x, we have tested only with 2.0.15 If you
download the precompiled linux binaries ensure you move cstranslate to bin/
and more the script dir to the root of the hhblits dir.
    cd hhsuite-2.0.15-linux-x86_64/
    cp lib/hh/bin/cstranslate bin/
    mv lib/hh/scripts/ ./
    mv lib/hh/data/ ./
It is ESSENTIAL that you ensure that hhblits and hhblitsdb.pl and hhblits are
working correctly once you have moved theses directories before you proceed.

Note: Metapsicov makes use of legacy blast NOT BLAST .

Note: You will also need the uniref90 database and the uniref100 database. You
need to prepare a blast database for uniref90 and use the hmmer esl-sfetch tool
to prepare the SSI index of the uniref100 database

Example usage:

cp 5ptp.fasta tmpdir/
run_metapsicov 5ptpA.fasta

Outputs:
5ptpA.metapsicov.stage2 - This file replicates the prior MetaPSICOV outputs
5ptpA.metapsicov.stage3 - This file contains the MetaPSICOV2 predictions

If you use this software for your research, please cite the following reference:

Improved protein contact predictions with the MetaPSICOV2 server in CASP12
Buchan, D.W.A., Jones, D.T. Proteins (2017) Sep 13. doi: 10.1002/prot.25379.

MetaPSICOV: Combining coevolution methods for accurate prediction of contacts
and long range hydrogen bonding in proteins
Jones, D.T., Singh, T., Kosciolek, T. & Tetchner, S.
Bioinformatics (2014) doi:10.1093/bioinformatics/btu791