A new method for finding the minimum free energy pathway (MFEP) of ions and small molecule transportation through a protein based on the three-dimensional reference interaction site model (3D-RISM) theory combined with the string method has been proposed. The 3D-RISM theory produces the distribution function, or the potential of mean force (PMF), for transporting substances around the given protein structures. By applying the string method to the PMF surface, one can readily determine the MFEP on the PMF surface. The method has been applied to consider the Na⁺ conduction pathway of channelrhodopsin as an example.

中文翻译：

---

基于3D-RISM理论和弦法的寻找离子的最小自由能途径和小分子通过蛋白质运输的新方法

提出了一种基于三维参考相互作用位点模型（3D-RISM）理论与弦法相结合的寻找离子的最小自由能途径（MFEP）和小分子通过蛋白质运输的新方法。3D-RISM理论产生用于在给定的蛋白质结构周围运输物质的分布函数或平均力（PMF）的潜力。通过对PMF表面应用串方法，可以轻松确定PMF表面上的MFEP。以该方法为例，以视紫红质的Na ⁺传导途径为例。