Software List

Data Collection and Processing

Structure Determination

  • AMoRe - Molecular replacement Local Manual
  • ARP/wARP (Automated Refinement and Chain Tracing) Web, Local Manual
  • BnP (Combines SnB and PHASES) Web, Paper
  • CCP4 (Collaborative Computing Project) Web, Local Manual 
  • CNS (Crystallography and NMR system) Web, Local Manual 
  • EPMR (Molecular replacement by evolutionary search) Local Manual
  • MAID (Assistant Electron Density Map Automated Tracing) Web, Local Manual
  • MOLREP (molecular replacement program) Web, Local Manual
  • phases (Phasing package, from Swami) Manual
  • SHARP (Statistical Heavy- Atom Refinement and Phasing) Web, Local Manual
  • SHELX (direct methods, heavy atoms search, and refinement) Web, Local Manual
  • SnB (A Direct-Methods Procedure for Determining Crystal Structures) Web, Manual
  • SOLVE/RESOLVE (Heavy atoms and MAD phasing package) Web, Local Manual
  • USF (Uppsala Software Factory) Web, Manual 

Structure Fitting

Structure Quality

  • AQUA (NMR model verification program) Web, Manual
  • Procheck (Stereochemical quality analysis software) Web, Manual
  • SFCHECK (Assessment between Structure Factors and models) Web, Local Manual
  • WHATIF Web, Manual

Visualization

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) 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) 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