Molecular Docking:
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在生物體中,要進行生化、催化或代謝反應時須要酵素(enzyme)和其接受體(substrate, ligand)結合後進行反應,其範圍包含甚廣。例如訊號傳遞(signal transduction)、荷爾蒙作用、脂肪酸的運送等。因為不同分子之間的彼此交互作用,例如蛋白質-蛋白質、蛋白質-核酸、蛋白質-脂肪酸等,而引發生許許多多的特定生化功能。當我們利用電腦來模擬各種結合的情形時,我們稱這一種技術為嵌合(docking)。嵌合方法在結構生物上的應用就是在藥物設計方面,找出可能的活化區(active site)、找出前驅物(lead compound)、突變(mutation)的影響等。利用此一方法可以有效率的減少在實驗上、設計上所須要花費的時間。


GEMDOCK

GEMDOCK - a Generic Evolutionary Method for molecular DOCKing. GEMDOCK is a program for computing a ligand conformation and orientation relative to the active site of target protein.


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.

pdb

Autodock plugin

This plugin should help to set up docking runs with Autodock and view docking results. It has two features:

  1. Setup of a docking grid for Autodock with PyMOL.
  2. View the docking results.

pdb

ZDOCK

ZDOCK searches all possible binding modes in the translational and rotational space between the two proteins and evaluates each pose using an energy-based scoring function.

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