Summary

• DockIt is robust and capable of high throughput runs.

 
• Runs are easy to set up. 3D coordinates are not needed for ligands.

 
• Parallel version (PVM based) provided. Single input and single output stream. Jobs spawned and results automically collected. Ideal for loosely coupled clusters.

 
• User specified distance constraints. Enforce particular interactions or covalent ligand binding.

 
• Need to balance parameters for the task at hand. For geometry prediction, use more random trials and include hydrogens (hydrogens typically increase runtime up to twofold).

 
• Different scoring functions (and different sets of run parameters) seem more suited to different tasks. PLP and PMF seem better to virtual screening.

Future directions

• Continued evaluation of scoring.

 
• Other scoring methods or consensus methods for combining multiple scoring methods.

 
• Plug in architecture for scoring. Will allow refinement against PLP function.

 

Version 1.0 is available. Evaluation copies can be provided.