Software packages developed in the laboratory.
The Bodil visualization and modeling package has its own web pages. See Bodil.
Creates 3D atomic coordinates from molecular connectivity via metric matrix distance geometry and confomer ensembles using a genetic algorithm. See Balloon.
ShaEP aligns (superimposes) two rigid 3D molecular structure models and computes a similarity index for the overlay. It can be used for the virtual screening of libraries of chemical structures against a known active molecule, or as a preparative step for 3D QSAR methods. See ShaEP.
McQSAR generates quantitative structure-activity relationships (QSARs) using the genetic function approximation paradigm. See McQSAR.
Contactos is a small Python program for calculating similarities between docking results. The similarity matrices output by Contactos can be used to cluster small-molecule docking results. See Contactos.
Malign and Malform
The Malign multiple sequence alignment program and the alignment formatting tool Malform can be downloaded as gzipped tar archives. The gzip compression tool is freely available from the Free Software Foundation. These archives contain the C source code and the instructions and makefiles to compile and install the software. Relevant bibliographic citations are provided in the README files in the archives. Note that the following programs and data available are covered by DISCLAIMER.
- MALIGN multiple sequence alignment program: malign.tar.gz
- MALFORM alignment formating tool for MALIGN: malform.tar.gz
- MULTI_GA_FIT structural alignment of 3D structures: multi_ga_fit.tar.gz
Matrices for comparing amino acid sequences
- Amino acid replacements from 127 families of aligned 3D structures: original data grouped by percentage identity: raw_127.h
- Sequence comparison matrices, amino acid replacements, grouped by percentage identity: total.h
- Sequence comparison matrices, amino acid replacements, accessible positions, grouped by percentage identity: access.h
- Sequence comparison matrices, amino acid replacements, inaccessible positions, grouped by percentage identity: inacc.h
- Sequence comparison matrices, assorted published matrices: mat11.h
- Download all of the above matrices in a single gzipped tar archive: matrices.tar.gz