SIRIUS
Sirius is a component-based visualization framework designed for application in molecular modeling, drug discovery, protein structure analysis, as well as database mining and sequence-based work. It is equally suited for protein and small molecule construction and visualization.
The primary features include:
- full support for structure building from fragments and peptide editor
- distance- and geometry-based addition of hydrogen atoms
- detection of hydrogen bonds and steric clashes
- command line interface
- scripting compatible with RasMol visualization of molecular dynamics trajectories
- support for multi-file simulations, real-time secondary structure and RMSD calculations
- export of trajectories as video protein structure alignment independent manipulation of displayed structures
- support for PDB, MOL2, SDF and other formats
- access to PDB, InterPro and Uniprot databases with interactive features sequence alignment editor capable of handling very large number of sequences export/import of the current display cross-viewer connectivity for common selection and coloring
Manual: http://sirius.sdsc.edu
INPUT = Protein Structure Coordinates; protein sequences in several formats
