The ModFOLDclustQ Model Quality Assessment Program -------------------------------------------------- Version 1.0 (Sept 2009) (c) Liam J. McGuffin, Daniel B. Roche Description ----------- You can only use this program if you have MULTIPLE models for your target sequence. ModFOLDclustQ works best if you have several models, if possible built from alternative target-template alignments, using several different methods. Clustering methods such as ModFOLDclustQ are currently the most accurate methods, but the ModFOLDclustQ results will not be as reliable if you only have a few models that have been built using the same target-template alignment. Please download the ModFOLD method if you only have a SINGLE model for your target sequence. References ---------- The following paper describes ModFOLDclustQ: McGuffin, L.J. & Roche, D.B. (2009) Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments. Bioinformatics, In press. Installation ------------ No installation is required for ModFOLDclustQ program itself after you have downloaded the file. The program is provided in the form of an executable jar file (ModFOLDclustQ.jar) and should run on most operating systems where Java is installed, however the instructions below refer to Linux/Unix based systems. Requirements: 1. A recent version of Java (java.com/getjava/). Running the program ------------------- You can edit the shell script (ModFOLDclustQ.sh) or you can follow the steps below. 1. (optional) Set the environment variable for Java, if you have not installed it system wide. e.g. export JAVA_HOME=/home/Liam/jdk1.6.0/ 2. Run ModFOLDclustQ. For example, if your target is called "T0515", the sequence file is "/home/liam/T0515.fasta" and the models directory is "/home/liam/T0515_example_models/", then enter the following: $JAVA_HOME/bin/java -jar ModFOLDclustQ.jar T0515 /home/liam/T0515.fasta /home/liam/T0515_example_models/ Or, if you have java installed system wide: java -jar ModFOLDclustQ.jar T0515 /home/liam/T0515.fasta /home/liam/T0515_example_models/ N.B. this will produce an unsorted output file which you can sort in Linux/Unix/OSX using: sort -g -r -k +2 T0515_ModFOLDclustQ.unsort > T0515_ModFOLDclustQ.sort Please ensure that the models are provided as separate files in PDB format. The sequence file should be in FASTA format. IMPORTANT: Please also note that you should use FULL PATHS for your input file and models directory, the models directory should also end with a "/". Output ------ An output file is produced in the models directory (e.g. "/home/liam/T0515_example_models/") and a log of the progress is written to the screen as standard output. The sorted data file consists of the target name plus "_ModFOLDclustQ.sort", e.g. "T0515_ModFOLDclustQ.sort". This file contains the same data as a QMODE2 file but without the headers and in a more convenient machine readable format. Trouble Shooting ---------------- Email me: l.j.mcguffin@reading.ac.uk I will try to respond to your issue as soon as I can! Thanks, Liam