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How to create a database to search for new ligand compounds from the three-dimensional structure database

机译:如何创建数据库以从三维结构数据库中搜索新的配体化合物

摘要

PPROBLEM TO BE SOLVED: To provide a method of generating a three-dimensional structure database, for use in searching ligand compounds of a biopolymer from a three-dimensional structure database. PSOLUTION: The method comprises a first step (i) of preparing dummy atoms at positions of hetero atoms which is to be the partner of hydrogen bonding of a hydrogen-bonding functional group, in accordance with the three-dimensional coordinates of a biopolymer; a second step (ii) of selecting one of trial compounds and comparing distances between dummy atoms with the distances between hydrogen-bonding hetero atoms in the trial compound, while varying conformation of the trial compound and docking the biopolymer and the trial compound to generate a structure of a complex, and evaluating an interaction between the biopolymer and the trial compound to search the most stable complex structure; a third step (iii) of deciding the trial compound as a ligand candidate compound, on the basis of the value of an interaction energy between the biopolymer and the trial compound in the most stable complex structure; and a fourth step (iv) of repeating the second and third steps for all trial compounds. PCOPYRIGHT: (C)2005,JPO&NCIPI
机译:<要解决的问题:提供一种生成三维结构数据库的方法,该方法用于从三维结构数据库中搜索生物聚合物的配体化合物。

解决方案:该方法包括第一步(i),根据a的三维坐标,在杂原子的位置制备拟原子,该杂原子将成为氢键合官能团的氢键结合的伙伴。生物聚合物第二步(ii),选择一种试验化合物,并将虚拟原子之间的距离与该试验化合物中氢键键合的杂原子之间的距离进行比较,同时改变该试验化合物的构型并将生物聚合物和该试验化合物对接,以生成一个复合物的结构,并评估生物聚合物与试验化合物之间的相互作用以寻找最稳定的复合物结构;第三步骤(iii),基于最稳定的络合物结构中生物聚合物与试验化合物之间的相互作用能的值,确定该试验化合物为配体候选化合物;第四步(iv),对所有试验化合物重复第二步和第三步。

版权:(C)2005,JPO&NCIPI

著录项

  • 公开/公告号JP3747048B2

    专利类型

  • 公开/公告日2006-02-22

    原文格式PDF

  • 申请/专利权人 板井 昭子;

    申请/专利号JP20040317749

  • 发明设计人 板井 昭子;水谷 実穂;

    申请日2004-11-01

  • 分类号G06F19;G06F17/30;

  • 国家 JP

  • 入库时间 2022-08-21 21:49:18

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