A flexible triangulation method to describe the solvent-accessible surface of biopolymers
A flexible triangulation method to describe the solvent-accessible surface of biopolymers
复制标题
描述生物聚合物可接触溶剂表面的灵活三角测量法
DOI：
10.1023/a:1016089901704
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发表时间：
1998-05-01
影响因子：
3.5
通讯作者：
Vogel, PJ
中科院分区：
文献类型：
--
作者：
Juffer, AH;Vogel, PJ
提出了一种相对简单的用于连续介质静电学应用的蛋白质溶剂可及表面三角测量方法——边界元法。第一。蛋白质被放置在具有特定晶格间距的三维晶格上。对于每个点阵点，分配一个方框。位于溶剂区和蛋白质内部的盒子从套装中移除。盒子之间的不适当连接和蛋白质内部可能存在的空洞会破坏三角形表面的适当连接。剩下的一组框定义了蛋白质的外部轮廓。在自由面定义的表面被平滑以更准确地遵循大分子的形状之后，暴露在剩余一组盒子的溶剂中的每个自由面都被三角化。最后一步是将三角形顶点映射到一组表面点上，这些点定义了溶剂可接近的表面。三角形顶点处的法向量也可以从定义曲面方向的自由面中获得。该算法测试了六种分子，包括四种蛋白质；一种二肽，由25个残基、钙结合蛋白、溶菌酶、钙调蛋白和角质酶组成的螺旋状肽。对于每个分子，计算了总面积，并与从点状溶剂可及表面计算的结果进行了比较。由于边界元法出于效率考虑，需要较少的顶点和三角形来减少未知的数量，因此三角形的数量不宜太高。然而，对于较大的晶格间距（0.30 nm），获得了可信的结果，相对误差不超过12%，而对于较小的晶格间距（低至0.16 nm），则接近于零。三角测量计算机程序（用c++编写）的输出相当简单，因此可以很容易地转换为任何分子图形程序可接受的任何格式。
A relatively simple protein solvent-accessible surface triangulation method for continuum electrostatics applications employing the boundary element method is presented. First. the protein is placed onto a three-dimensional lattice with a specified lattice spacing. To each lattice point, a box is assigned. Boxes located in the solvent region and in the interior of the protein are removed from the set. Improper connections between boxes and the possible existence of cavities in the interior of the protein which would destroy the proper connectivity of the triangulated surface are taken care of. The remaining set of boxes define the outer contour of the protein. Each free face exposed to the solvent of the remaining set of boxes is triangulated after the surface defined by the free faces has been smoothed to follow the shape of the macromolecule more accurately. The final step consists of a mapping of triangle vertices onto a set of surface points which define the solvent-accessible surface. Normal vectors at triangle vertices are obtained also from the free faces which define the orientation of the surface. The algorithm was tested for six molecules including four proteins; a dipeptide, a helical peptide consisting of 25 residues, calbindin, lysozyme, calmodulin and cutinase. For each molecule, total areas have been calculated and compared with the result computed from a dotted solvent-accessible surface. Since the boundary element method requires a low number of vertices and triangles to reduce the number of unknowns for reasons of efficiency, the number of triangles should not be too high. Nevertheless, credible results are obtained for the total area with relative errors not exceeding 12% for a large lattice spacing (0.30 nm) while close to zero for a smaller lattice spacing (down to 0.16 nm). The output of the triangulation computer program (written in C++) is rather simple so that it can be easily converted to any format acceptable for any molecular graphics programs.