AutoDock Set-up and Analysis

• ADT / AutoDockTools — designed for AutoDock and AutoGrid. It is built on Michel Sanner's PMV, and is available in two forms:
• Graphical User Interface (GUI)
  
• Python Scripts
  
• Both the GUI and the Python scripts can be used to:
• prepare the ligand input PDBQ and PDBQT files for AutoDock
• prepare the receptor input PDBQS and PDBQT files for AutoGrid
• create grid parameter files (GPF) to set up AutoGrid calculations
• create docking parameter files (DPF) for AutoDock calculations
• analyse the docking results from AutoDock log files (DLG)
• isocontour AutoGrid maps to assist in understanding ligand binding and in designing more potent inhibitors

• BDT — ("Blind Docking Tool") third-party GUI software that can:
• combine AutoGrid maps for different sctructures, to account for flexibility in the receptor
• make staggered non-overlapping sets of AutoGrid maps, to cover a very large receptor when performing blind docking
• help to set up AutoDock input files for virtual screening of a library of molecules against one or more receptors

Hydrogens, Hydrogen-Bond Networks and Waters

• MolProbity is a great web-accessible front-end to REDUCE, that is useful for:
• evaluating the quality of your protein structure
• adding hydrogens
• optimising the hydrogen-bond network by flipping Asn, Gln amido groups and His imidazole rings by 180º. This can be very valuable before running AutoGrid, because sometimes crystal structures do not have the best placement of such sidechains.
• REDUCE citation:
• Word JM, Lovell, SC, Richardson, JS, and Richardson, DC (1999) "Asparagine and glutamine: using hydrogen atom contacts in the choice of sidechain amide orientation" J. Mol. Biol. 285, 1733-1745.

• PDB2PQR converts PDB files into PQR files (used by APBS, for example), but is also "an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations". PDB2PQR is useful for:

• Adding a limited number of missing heavy atoms to biomolecular structures
• Determining side-chain pKa values & Adding hydrogens at a specific pH
• Placing missing hydrogens
• Optimizing the protein for favorable hydrogen bonding
• Adding partial charge and radius parameters for the following forcefields:
  
• AMBER
• CHARMM
• PARSE
• TYL06
• PDB2PQR is an open source project.
• PDB2PQR citation:
• Dolinsky TJ, Nielsen JE, McCammon JA, and Baker NA (2004). PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research, 32, W665-W667.
  
• PROPKA performs pKa calculations, useful for deciding on the correct protonation state for ionisable sidechains. (PROPKA is used by PDB2PQR.)
• PROPKA citation:

• Hui Li, Andrew D. Robertson, and Jan H. Jensen (2005). Very Fast Empirical Prediction and Interpretation of Protein pKa Values. Proteins, 61, 704-721.

• DOWSER
• predicts & optimizes the positions and orientations of internal, buried water molecules
• automatically adds polar hydrogens are ed to the structure
• extended to work with DNA by Andy McCammon's Group member Cameron Mura

• SOLVATE
  
• constructs "an atomic solvent environment model for a given atomic macromolecule model for use in molecular dynamics simulations", and can place salt ions, and buried waters, too.

• * HBPLUS
  
• is a hydrogen bond calculation program "calculates hydrogen positions, deals with hydrogens that can occupy more than one position; optionaly includes amino-aromatic H-bonds" and "analyses H-bonding Near Asn, Gln and His Side-Chains and suggests optimal conformations".

Databases

• Databases

Tools

• Tools