Centre for Molecular Design (CMD)


The software on this page is distributed under the terms of the GNU General Public License.


APTE is a Perl program that locates potential A-form DNA promoter transcription elements in genomes. It identifies blocks within a DNA sequence with negative A-DNA propensity energy (Basham et al. PNAS, 92, 6464, 1995) that precede a specified promoter motif upstream of a transcription start site. Input sequences may be read from a GFF3 file or an Ensembl MySQL database.

README [Text (.txt) - Mon, 17 Sep 2012 09:50:00 BST]

apte [Text (.txt) - Tue, 10 Jun 2014 08:30:00 BST]


Dash is a technique for analysing molecular dynamics simulations based on the torsion angles of rotatable bonds. It describes the major features of a trajectory as a sequence of transitions between states representing molecular conformations. Dot is a companion program that regenerates pseudo-trajectories from Dash-compressed trajectories. For further details see:

D. W. Salt, B. D. Hudson, L. Banting, M. J. Ellis and M. G. Ford
DASH: A novel analysis method for molecular dynamics simulation data. Analysis of ligands of PPAR-gamma.
J. Med. Chem., 48, 3214-3220, 2005.

Current Release

README.md [Text (.txt) - Tue, 18 Oct 2016 13:31:00 BST]

mdash-3.0.0.tar.bz2 [Text (.txt) - 1.6MB Tue, 18 Oct 2016 13:36:00 BST]

mdash-3.0.0.zip [ZIP (.zip) - 2.1MB Tue, 18 Oct 2016 13:38:00 BST]

CHECKSUMS [Text (.txt) - Tue, 18 Oct 2016 13:40:00 BST]

Original Release

README [Text (.txt) - Fri, 02 May 2014 11:02:00 BST]

dash-1.1.tar.bz2 [Text (.txt) - 0.9 MB Fri, 02 May 2014 13:20:00 BST]

dash-1.1.tar.gz [Text (.txt) - 1.2 MB Fri, 02 May 2014 13:20:00 BST]

dash-1.1.zip [Text (.txt) - 1.2 MB Fri, 02 May 2014 13:20:00 BST]


Trepan is a Matlab program for extracting decision trees from Neural Networks. For further details see the Trepan project home page.

README [Text (.txt) - Mon, 03 Dec 2007 11:42:00 GMT]

trepan-1.0.tar.gz [Text (.txt) - 368 KB Mon, 03 Dec 2007 11:44:00 GMT]

trepan-1.0.zip [Text (.txt) - 378 KB Mon, 03 Dec 2007 11:47:00 GMT]

Unsupervised Forward Selection

Unsupervised forward selection is a data reduction procedure used for eliminating redundant variables in QSAR analyses. For examples of its use see:

D. C. Whitley, M. G. Ford and D. J. Livingstone
Unsupervised Forward Selection: A Method for Eliminating Redundant Variables
J. Chem. Inf. Comp. Sci., 40, 1160-1168, 2000.

README [Text (.txt) - Mon, 03 Dec 2007 11:52:00 GMT]

ufs-1.8.tar.gz [Text (.txt) - 169 KB Mon, 03 Dec 2007 11:53:00 GMT]

ufs-1.8.zip [Text (.txt) - 175 KB Mon, 03 Dec 2007 11:55:00 GMT]