Centre for Molecular Design (CMD)

Software

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

APTE

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.

Dash

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.

Trepan

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

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.