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AUTODOCK


AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. It is free for academic.
 


Main applications:

  • Binding mode prediction of ligands in a protein environment It includes 2 methods : a Monte Carlo simulated annealing and a Lamarcian genetic algorithm
  • Automated high-throughput screening
     


References:

Morris, G. M., Goodsell, D. S., Halliday, R.S., Huey, R., Hart, W. E., Belew, R. K. and Olson, A. J. (1998), J. Computational Chemistry, 19: 1639-1662. "Automated Docking Using a Lamarckian Genetic Algorithm and and Empirical Binding Free Energy Function".
 
w3.to/autodock


ZINC


ZINC is a free database of commercially-available compounds for virtual screening. ZINC contains over 3.3 million compounds in ready-to-dock. Compounds in ZINC may be ordered directly from the vendors.
 


References:

Irwin and Shoichet, J. Chem. Inf. Model. 2005;45(1):177-82
 
blaster.docking.org/zinc


PDB


PDB is the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data. Malaria target structures from PDB were improved by SCAI for the Data Challenge
 


References:

H.M.Berman, J.Westbrook, Z.Feng, G.Gilliland, T.N.Bhat, H.Weissig, I.N.Shindyalov, P.E.Bourne
The Protein Data Bank
Nucleic Acids Research, 28 pp. 235-242 (2000)
 
www.pdb.org


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