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GREEN: A program package for docking studies in rational drug design

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Summary

A program package, GREEN, has been developed that enables docking studies between ligand molecules and a protein molecule. Based on the structure of the protein molecule, the physical and chemical environment of the ligand-binding site is expressed as three-dimensional grid-point data. The grid-point data are used for the real-time evaluation of the protein-ligand interaction energy, as well as for the graphical representation of the binding-site environment. The interactive docking operation is facilitated by various built-in functions, such as energy minimization, energy contribution analysis and logging of the manipulation trajectory. Interactive modeling functions are incorporated for designing new ligand molecules while considering the binding-site environment and the protein-ligand interaction. As an example of the application of GREEN, a docking study is presented on the complex between trypsin and a synthetic trypsin inhibitor. The program package will be useful for rational drug design, based on the 3D structure of the target protein.

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Authors and Affiliations

  1. Faculty of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, 113, Tokyo, Japan

    Nobuo Tomioka & Akiko Itai

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  1. Nobuo Tomioka
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  2. Akiko Itai
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Tomioka, N., Itai, A. GREEN: A program package for docking studies in rational drug design. J Computer-Aided Mol Des 8, 347–366 (1994). https://doi.org/10.1007/BF00125372

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  • DOI: https://doi.org/10.1007/BF00125372

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