Macromolecular Interactions

Docking Programs

• APROPOS: (Automatic PROtein POcket Search), by C. Frömmel. Institute Biochemistry, Medical Faculty, Humboldt-University of Berlin.
  Based purely on geometric criteria.
  
  
• AUTODOCK: (Automated Docking of Ligands to Macromolecules)
  Program written by D.S. Goodsell, Arthur J. Olson's Laboratory.
  • Olson's Group: Molecular Graphics Laboratory.
    G.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.
  • E. 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 4.0.
  • The DOCK FAQ.
  
  
• CombiBUILD: Fragment-based docking.
  Home Page. A structure-based drug design program created to aid the design of combinatorial libraries.

• ESCHER: Evaluation of Surface Complementarity, Hydrogen-bonding, Electrostatic interaction in molecular Recognition. 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.
  German National Research Center for Information Technology, Institute for Algoritms and 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)
  
  
• FTDock: (Fourier Transform Docking)
  Biomolecular Modelling Laboratory, Imperial Cancer Research Fund. (London)
  • 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)
  • I. Vakser's Home Page.
  • GRAMM v1.03
  
  
• HEX: an interactive protein docking and molecular superposition program. The main thing which distinguishes Hex from other macromolecular (i.e. protein and DNA) docking programs and molecular graphics packages is its use of spherical polar Fourier correlations to accelerate docking calculations.
  • Home Page
  
  
• HotDock: (An Interactive Approach to Molecular Docking)
  University of Paderborn.
  • HotDock Home Page.
  
  
• LIGIN:
  • The EMBL Sander Group: Home Page.
  • Ligin.
  
  
• PUZZLE: Method for Protein Docking Based on Surface Shape Complementarity (1994).
  • A. Tramontano's Home Page. Istituto di Ricerche di Biologia Molecolare (Rome).
  • Docking Home Page.
  
  
• STALK: A System for Modeling Protein-Protein Interactions.
  • STALK Home Page.

Other Docking Links

• B. Duncan and A. Olson: ``Predicting Protein-Protein Interactions using Parametric Surfaces''(1994), The Scripps Research Institute.
• H.P. Lenhof: The Protein Docking Problem (in German), Max-Planck-Institut fur Informatik.
• E. Moret: Home Page. CMC Group; Department of Pharmaceutical Chemistry. Utrecht University (The Nederlands).
• G.M. Morris: Home Page. The Scripps Research Institute.
• A.P. Singh: Protein Docking References, including abstracts.
• Viwish: Home Page. A visualisation server for protein modelling and docking, by T. Klein, F. Ackermann, and S. Posch.
• H. Wolfson: Home Page. Computer Science Department, School of Mathematical Sciences, Tel-Aviv University.

Related Databases

• LIGAND: Ligand Database. GenomeNet, Institute for Chemical Research, Kyoto University, Japan.
• LIGPLOT v4.0: A Program for Automatically plotting Protein-Ligand Interactions. A. Wallace and R. Laskowski. Home Page.
• NUCPLOT: A program to generate schematic diagrams of protein-nucleic acid interactions, written by N.M. Luscombe and R.A. Laskowski.
• Find-NCB: Noncovalent Bond Finder. Displays the closest contacts to ligand or interface, reports distances and walks over water bridges.

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