Development
   System Information

1. Using ZDOCKpro in Insight II

   How ZDOCKpro works
   Preparing the input structure data
   How to run ZDOCK
      Angular step of rotational sampling
      Blocking residues
      Filtering residues
         The order of specifed residues
   How to run RDOCK
      Output file
   Analyzing the output
      ZDOCK
      RDOCK
   Performance benchmark
   Command summary
      ZDOCK pulldown
         Run_ZDOCK
         Filter
         LoadZTable
         LoadZResults
      RDOCK pulldown
         Run_RDOCK
         LoadRTable
         LoadRResults
      Background_Job pulldown

2. Using ZDOCKpro standalone

   How ZDOCKpro works
      The ZDOCK process
      The RDOCK process
   Preparing the input structure data
   How to run ZDOCK
      Angular step of rotational sampling
      Blocking residues
      Filtering residues
      Creating coordinates for complexes using create_lig
   How to run RDOCK
      Output file
      Reranking poses
      Distributing the minimization to reduce calculation time
   Analyzing the output
      ZDOCK
      RDOCK
   Performance benchmark
   Command summary
      ZDOCK
      filterHits
      RDOCK
      create_lig
      rerank

3. ZDOCKpro in Insight tutorial

   Lesson 1: Rigid-body docking using ZDOCK
   Lesson 2: Filtering ZDOCK poses and RDOCK refinement
   Lesson 3: Analyze RDOCK results

4. Theory

   ZDOCK
      Pairwise Shape Complementarity (PSC)
      Search procedure
      Blocking and filtering steps
   RDOCK
      Energy minimization of ZDOCK complexes
      Electrostatic and desolvation energy

A. References

B. File Formats

   Input files
      ZDOCK standalone input PDB files
      ZDOCK standalone block residue and filterHits input files
         PDB format
         BU format
      uniCHARMM
   Output files
      ZDOCK and filterHits output file
      Intermediate PDB files
      RDOCK output file
      CHARMm minimized receptor and ligand PDB files
      Rerank output (standalone only)

Index

© 2005 Accelrys Software Inc.