Macromolecular interactions & Docking:

Docking Programs :

• APROPOS. ( Automatic PROtein POcket Search )
  Prof. Dr. Cornelius Frömmel. Institute Biochemistry, Medical Faculty, Humboldt-University of Berlin.
  Based purely on geometric criteria.
  
  
• AUTODOCK. ( Automated Docking of Ligands to Macromolecules )
  Original program written by David S. Goodsell in Arthur J. Olson's Laboratory.
  • Olson's Group : Molecular Graphics Laboratory.
    Garret M. Morris : Molecular Docking Web.
  • AutoDock Home Page.
  • AutoDock Results. Results of 100 independent docking runs of AutoDock 2.4, applied to a variety of ligand-protein systems.
  • Ed Moret has used Autodock in some interesting and animated dockings.
  
  
• DOCK.
  Department of Pharmaceutical Chemistry, School of Pharmacy, University of California.
  • Kuntz Research Group : Welcome Page.
  • DOCK Home Page
  • The DOCK Algorithms : DOCK 3.5.
  • The DOCK FAQ.
  
  
• ESCHER. Ausiello et al. 1997; Proteins: Struct. Funct. Genet.
  
  
• FlexiDock.
  University of Wisconsin Molecular Modelling Laboratory.
  • FlexiDock Contents
  • FlexiDock en SYBYL/Biopolymer : Tripos.
  
  
• FLExX. (Flexible Docking Method Using an Incremental Construction Algorithm. 1996). FlexX Home Page.
  (Rarey/Kramer/Lengauer/Klebe ) German National Research Center for Information Technology, Institute for Algoritms & Scientific Computing.
  
  
• FLOG. A system to select "quasi flexible" ligands complementary to a receptor if known three-dimensional structure. J.Comput.Aided Mol.Des. 8, 153-174 ( 1994 ). Miller; Kearsley; Underwood & Sheridan
  
  
• FTDOCK. ( Fourier Transform Docking )
  Biomolecular Modelling Laboratory, Imperial Cancer Research Fund., London, UK
  • ftdock Home Page.
  
  
• GOLD. ( Genetic Optimisation for Ligand Docking ).
  Docking program based on the algorithm described by Jones et al. J.Mol.Biol 254, 43-53 ( 1995 ).
  • GOLD Home Page.
  
  
• GRAMM. ( Global Range Molecular Matching )
  Medical University of South Carolina. Charleston.
  • Ilya Vakser : Home Page. Protein Docking Studies: Research.
  • GRAMM v1.03
  
  
• HotDock. ( An Interactive Approach to Molecular Docking )
  University of Paderborn.
  • HotDock Home Page.
  
  
• LIGIN.
  • The EMBL Sander Group : Sander Group's Home Page.
  • Ligin.
  
  
• PUZZLE. ( Helmer-Citterich/Tramontano ). Method for Protein Docking Based on Surface Shape Complementarity. 1994.
  • Anna Tramontano : Home Page. IRBM = Istituto di Ricerche di Biologia Molecolare ( Rome ).
  • Docking Home Page.
  
  
• STALK. ( Levine Group ) A System for Modeling Protein-Protein Interactions.
  • STALK Home Page.

Other Related Links :

• LIGAND : Ligand Database. GenomeNet, Institute for Chemical Research, Kyoto University, Japan.
• LIGPLOT v4.0 : A Program for Automatically plotting Protein-Ligand Interactions. A. Wallace & R. Laskowski. Home Page.
• Find-NCB : Noncovalent Bond Finder. Displays the closest contacts to ligand or interface, reports distances and walks over water bridges.
• Dr. Hans-Peter Lenhof's Home Page. Max-Planck-Institut fur Informatik. Saarbrucken. Germany.
• Dr. Ed E. Moret : Home Page. CMC Group ; Department of Pharmaceutical Chemistry. Utrecht University. The Nederlands.
• Dr. Haim Wolfson : Home Page. Computer Science Department, School of Mathematical Sciences, Tel-Aviv University.

Bibliography :

• DOCK program References.
• B. Duncan - A. Olson ( 1994 ): Predicting Protein-Protein Interactions using Parametric Surfaces. ( The Scripps Research Institute. La Jolla ).
• Daniel Fischer : List of Publications.