SAP : Pairwise structure alignment via double dynamic programming

References

Users publishing results obtained with the program and its applications should acknowledge its use by the following citation:

• Taylor W.R., Protein structure comparison using iterated double dynamic programming. Protein Sci. 8 (1999) 654-665.

• Taylor W.R., Protein structure comparison using SAP. Methods Mol. Biol. 143 (2000) 19-32.

Install / Uninstall

Please read the general ‘INSTALL’ instructions. For documentation execute ‘doxygen doxygen.cfg’ in the ‘src’ directory. Documentation files are created in ‘doc/html’ and ‘doc/latex’. The latex documentation is completed by executing ‘make pdf’ in the ‘doc/latex’ directory, which creates ‘refman.ps’ and ‘refman.pdf’.

Usage

sap <PDB_1> <PDB_2>
sap <PDB_1> <PDB_2> <one2one>

‘one2one’ is an optional integer value added to the diagonal; any negative value selects the default value of 1000.

Web Server

http://mathbio.crick.ac.uk/wiki/SAP

Authorship

• (C) 1999 W.R. Taylor (program author)
• (C) 2007 Alessandro Pandini : SAP web server
• (C) 2007 Jens Kleinjung : code release
• (C) 2008 Siv Hollup : code update to ANSI C standard

Availability

The program is made available under the GNU Public License for academic scientific purposes, under the condition that proper acknowledgement is made to the authors of the program in publications resulting from the use of the program.

License

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 3 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, see http://www.gnu.org/licenses/.