Tutorials:

• COMBINE analysis to derive protein structure-based QSARs
• GRID for structure-based drug design
• UHBD to compute electrostatic binding free energy
• 3DFS to do a flexible ligand pharmacophore search

Software:

• SYCAMORE: SYstems biology's Computational Analysis and MOdeling Research Environment
  

• RAMD Implementations
  

• AMBER: Patches
  

• NAMD: Scripts
  

• metaPocket:webserver to identify pockets on protein surfaces to predict binding sites for ligands
  

• LIGIN: Molecular docking using surface complementarity
  

• TRAJAN: A Tool to Analyze Trajectories from Molecular Simulations
  

• MolSurfer: 2D Maps to Navigate 3D Structures of Proteins and their Complexes
  

• ADS: Analytically Defined molecular Surfaces
  

• PIPSA: Protein Interaction Property Similarity Analysis
  

• SDA: Simulation of Diffusional Association
  

• ECM: Effective (potential derived) Charges for Macromolecules in solvent
  

• Our scripts for protein pKa calculations with the UHBD program