From Bioinformatics.Org Wiki
- Abacus - a no-frills program developed to investigate the significance of the putative correspondence between exons and units of protein structure.
- caRNAc - RNA secondary structure inference for set of homologous sequences
- caRNAsta - "Comparative Analysis of RNA structures by Tree Alignment"
- Chimera - excellent molecular graphics package with support for a wide range of operations
- CNS - the "Crystallography & NMR System" for macromolecular structure anaylsis
- cove - an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.
- Garlic - a free molecular visualization program
- LIBELLULA - a neural network based web server to evaluate fold recognition results
- MODELLER - a program for homology protein structure modelling by satisfaction of spatial restraints.
- ModView - a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
- MOPAC7 - a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions.
- PyMol - a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations
- RNA GENiE - a web based program for the prediction of rna genes in genomic DNA sequences
- RnaViz - a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules