Gabdoulline R R, Wade R C
European Molecular Biology Laboratory, Heidelberg, Germany.
J Mol Graph. 1996 Dec;14(6):341-53, 374-5. doi: 10.1016/s0263-7855(97)00008-8.
Molecular surfaces are widely used for characterizing molecules and displaying and quantifying their interaction properties. Here we consider molecular surfaces defined as isocontours of a function (a sum of exponential functions centered on each atom) that approximately represents electron density. The smoothness is advantageous for surface mapping of molecular properties (e.g., electrostatic potential). By varying parameters, these surfaces can be constructed to represent the van der Waals or solvent-accessible surface of a molecular with any accuracy. We describe numerical algorithms to operate on the analytically defined surfaces. Two applications are considered: (1) We define and locate extremal points of molecular properties on the surfaces. The extremal points provide a compact representation of a property on a surface, obviating the necessity to compute values of the property on an array of surface points as is usually done; (2) a molecular surface patch or interface is projected onto a flat surface (by introducing curvilinear coordinates) with approximate conservation of area for analysis purposes. Applications to studies of protein-protein interactions are described.
分子表面被广泛用于表征分子以及展示和量化它们的相互作用特性。在这里，我们考虑将分子表面定义为一个函数（以每个原子为中心的指数函数之和）的等值线，该函数近似表示电子密度。这种平滑性有利于分子性质（例如静电势）的表面映射。通过改变参数，可以构建这些表面以任意精度表示分子的范德华表面或溶剂可及表面。我们描述了在解析定义的表面上进行操作的数值算法。考虑了两个应用：（1）我们在表面上定义并定位分子性质的极值点。这些极值点在表面上提供了性质的紧凑表示，无需像通常那样在表面点阵列上计算性质的值；（2）为了分析目的，通过引入曲线坐标将分子表面补丁或界面投影到平面上，面积近似守恒。描述了在蛋白质 - 蛋白质相互作用研究中的应用。
