************************************************************************* * * * PROQ * * * * PROtein Quality predictor * * * * * * Version 1.0 (December 12, 2002) * * Version 1.1 (November 3, 2003) * * Version 1.2 (October 12, 2004) * * * * Björn Wallner * * Stockholm Bioinformatics Center * * SWEDEN * * * * Copyright (c) 2002 * * * ************************************************************************* * * * This program is free software; you can redistribute * * it and/or modify it under the terms of the GNU General Public License * * as published by the Free Software Foundation; either version 2 of the * * License, or (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, but * * WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * * General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program; if not, write to the Free Software * * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 * * USA * * * * Comments and suggestions may be sent to the e-mail address * * 'bjorn@sbc.su.se' * * * * * * * ************************************************************************* Citation -------- Please cite the following paper when using ProQ: Wallner B. and Elofsson A. "Can correct protein models be identified?", Protein Science, submitted October 2002. Installation ------------ To unpack tarball: tar -xzvf ProQv1.2.tar.gz In order to run the program you need two additional programs: Naccess and STRIDE. Naccess can be downloaded from http://wolf.bms.umist.ac.uk/naccess/. Follow instructions on the web page. STRIDE from ftp://ftp.ebi.ac.uk//pub/software/unix/stride/src/stride.tar.gz. * Place the file in a empty directory tar -xvzf stride.tar.gz make * You should now have file named "stride" in that directory. For ProQ to run you need to specify where it is located, where Naccess and STRIDE are located and a temporary directory. Add these lines to your .bashrc or .tschrc. Please observe that PROQ_DIR is changed to PROQ_DIR12, in order not to accidently run the old version. bash: export PROQ_DIR12=full_PROQ_DIR_path export NACCESS=full_path_to_the_nacces_script export STRIDE=full_path_to_the_stride_executable export TMPDIR=full_path_to_temporary_directory (needs to be created before) tsch: setenv PROQ_DIR12 full_PROQ_DIR_path setenv NACCESS full_path_to_the_nacces_script setenv STRIDE full_path_to_the_stride_executable setenv TMPDIR full_path_to_temporary_directory (needs to be created before) To get optimal performance secondary structure should be predicted using PSIPRED: ftp://bioinf.cs.ucl.ac.uk/pub/psipred/. ProQ can use two formats: the output file from PSIPRED with the horizontal format. Ex: Conf: 946899846566678999999999984078872366414068999996789999879998 Pred: CCHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCHHCCCCCCCCHHHHHHECCCCC AA: INTITFDVGNATINKYATFMKSIHNQAKDPTLKCYGIPMLPNTNLTPKYLLVTLQDSSLK 10 20 30 40 50 60 Conf: 799999756948887865899987688758998633011210014788720022342688 Pred: HHHHHHECCCHHHHHHECCCCCCCHHHHCCCCCCCCHHHHHHCCCCCCCCHHHHCCCCCC AA: TITLMLKRNNLYVMGYADTYNGKCRYHIFKDISNTTERNDVMTTLCPNPSSRVGKNINYD 70 80 90 100 110 120 or a file with only the secondary structure assignments Ex: CCHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCHHCCCCCCCCHHHHHHECCCCC HHHHHHECCCHHHHHHECCCCCCCHHHHCCCCCCCCHHHHHHCCCCCCCCHHHHCCCCCC Usage ----- ProQ -model [model file] optional: -ss [ssfile or psipred file] -CA [CA-model] -frac [fraction modelled] -output [short/long(default)] -model The model you want to evaluate optional parameters (using these parameters will increase performance) OBS It is really recommended using at least secondary structure. -ss predicted secondary structure file (for formats see above) -CA If you are doing homology modelling comparing the full atom model with a CA model from the aligned residues in template might improve the performance slightly (not as much as secondary structures) -frac (length of model)/(length of query sequence), this makes the MaxSub prediction more relaible. -output if "short" only LGscore MaxSub will be printed. Example runs: Run ProQ with predicted secondary structure ./ProQ -model test.pdb -ss test.ss Run ProQ without predicted secondary structure ./ProQ -model test.pdb Run ProQ with predicted secondary structure and frac the model is only 50% of the query sequence. ./ProQ -model test.pdb -ss test.ss -frac 0.5