Software

Modeling

• Amber (molecular dynamics simulations)  Web, Local Manual
• DSSP (Kabsch and Sander Secondary Structure Assignment) Web, Local Manual
• ESPript (interface for visualization of secondary structure) Web, Local Manual
• DOCK Web, Local Manual
• FTDOCK Web, Local Manual
• GRASP (Graphical Representation and Analysis of Structural Properties) Web, Local Manual
• JNET (secondary structure prediction) Web, Local Manual
• HBPLUS (hydrogen bonds building, for LIGPLOT) Web
• LIGPLOT (ligand plot for a PDB file) Web, Local Manual
• Liged (Java applet for ligand editing) Local Manual
• MAGE (3D Macromolecule Analysis) Web, Local Manual
• MODELLER (Comparative Protein Structure Modeling by Satisfaction of Spatial Restraints) Web, Local Manual
• MSP (Molecular Surface Package) Web, Local Manual
• Ribbons (Molecular graphics software) Web, Local Manual
• PHD (secondary structure prediction) Web
• PROSPECT (prediction by threading toolkits) Web
• THREADER (Homolog structure prediction) Web , Local Manual
• TOPS (Topological cartoon computing) Web