Red - Costware Green- Freeware/Shareware
|
Program Name |
Brief Description |
| 3DNA | 3DNA is a versatile package for analyzing and rebuilding 3-dimensional nucleic acid structures. In the core, it uses a simple, yet mathematically rigorous and geometrically meaningful, scheme for calculating local base-pair, step, and helical parameters, and exact rebuilding of a structure based on these parameters. Unique features of 3DNA include automatic classification of a dinucleotide step as A-, B- or TA-like based on the positioning of the phosphorus atoms, and the generation of ``standardized'' base stacking diagrams. The rebuilding routines give Calladine-Drew style schematic representations of DNA as well as full atomic models with sugar-phosphate backbone. |
| B (previously Biomer) | B is a Java-based, on-line biomolecular modeling package. It should be useful in generating initial structures of biopolymers and small organic molecules. Simple force-field energy minimizations can be carried out in addition to simulated annealing with molecular dynamics. |
| DNA Star | The DNA Structural Bioinformatics Web Server |
| Escher NG | ESCHER Next Generation (NG) is an enhanced version of the original ESCHER protein-protein automatic docking system developed in 1997 by Gabriele Ausiello, Gianni Cesareni and Manuela Helmer Citterich. The new release, with a reengineered code, includes some new features such as DNA-Protein docking. |
| Namot | Namot (Nucleic Acid MOdeling Tool) is a program to allow users to manipulate molecular models of nucleic acids based on a set of reduced co-ordinates developed at Los Alamos National Laboratory and the Max Planck Institute for Biophysical Chemistry |
| Vega | VEGA was developed to create a bridge between most of the molecular software packages, like BioDock, Quanta/CHARMm, Insight II, MoPac, etc. In this tool have been also implemented some features that are useful to analyze, display and manage the 3D structures of molecules. |