Instructions for building MUSTANG
Dependencies: GNUMake or equivalent. A modern C++ compiler. MUSTANG is known to build with G++ >=4.1.2. If these dependencies are met, follow these instructions:
- Download the source code from the link above.
- Extract the archive with:
tar -zxvf mustang_v3.2.3.tgz
- Type: cd MUSTANG_v3.2.3
- Build MUSTANG with: make
- The built binary will appear in the bin/ subdirectory.
- Test the binary by running from MUSTANG_v3.2.3/ directory:
./bin/mustang-3.2.3 -f data/test/test_zf-CCHH
- This should produce the following files:
Copyright (c) 2005-, Arun Konagurthu, Monash University. arun DOT konagurthu AT monash DOT edu http://lcb.infotech.monash.edu.au/mustang All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the University of Melbourne nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESSINTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Command line options
Mustang is a program that implements an algorithm for structural alignment of multiple protein structures. Given a set of PDB files, the program uses the spatial information in the Calpha atoms of the set to produce a sequence alignment. Based on a progressive pairwise heuristic the algorithm then proceeds through a number of refinement passes. Mustang reports the multiple sequence alignment and the corresponding superposition of structures.
To keep the command line short the user can write the path and file names into a (description) file and supply the description file at the command line using the '-f' option. For example see the file used to test the installation: '/usr/share/doc/mustang/examples/test_zf-CCHH'.
PATH should have a prefix '>'. When the program parses this file, it looks for the line starting with '>' symbol (whitespaces are ignored before and after the symbol). The PATH containing the PDB files of the structures to be aligned should follow. See for example: /usr/share/doc/mustang/examples/test_zf-CCHH'.
FILENAMES should have a prefix '+' (whitespaces are ignored before and after this symbol). If PATH is specified then only the filenames should be provided after the '+' symbol. However, if PATH line is NOT provided, then the absolute/relative paths of the structure files should be provided.
REFERENCEA. S. Konagurthu, J. Whisstock, P. J. Stuckey, and A. M. Lesk, MUSTANG: A multiple structural alignment algorithm, Proteins, 64(3) 559-574 (2006).
Paper describing the MUSTANG algorithm