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Method for calculating bond free energy, apparatus for calculating binding free energy, program, and method for screening compounds
Method for calculating bond free energy, apparatus for calculating binding free energy, program, and method for screening compounds
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机译:计算键自由能的方法,计算键自由能的装置,程序和筛选化合物的方法
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摘要
A calculation method of binding free energy, which includes: calculating solvation energy (”G 1 ) between a solvent and a compound; and calculating an energy change (”G 2 ) between a bound state (»=0) where the compound and a protein are bound, and an unbound state (»=1) where the compound and the protein are not bound, wherein the calculating the energy change (”G 2 ) includes: determining a distance (D th ), within which structure sampling is performed; calculating a change in binding energy (”G 21 ) between the compound and the protein within a distance equal to or shorter than the distance (D th ), calculating a change in solvation energy (”G 23 ) between the solvent and the compound with ignoring an influence of the protein, calculating a change in binding energy (”G 22 ) between the compound and the protein with interpolation, and calculating a correction term (”G 24 ) with respect to a standard state.
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机译:结合自由能的计算方法,包括:计算溶剂与化合物之间的溶剂化能(“ G 1”);计算在化合物与蛋白质结合的结合状态(»= 0)与在未结合化合物与蛋白质的未结合状态(»= 1)之间的能量变化(“ G 2”),能量变化(“ G 2”)包括:确定距离(D th),在该距离内进行结构采样;在等于或小于距离(D th)的距离内计算化合物与蛋白质之间的结合能(“ G 23)的变化,计算溶剂与化合物之间的溶剂化能(” G 23)的变化,忽略蛋白质的影响,通过内插法计算化合物与蛋白质之间的结合能(“ G 22”)的变化,并针对标准状态计算校正项(“ G 24”)。
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