On the computation of molecular surface correlations for protein docking using fourier techniques.
On the computation of molecular surface correlations for protein docking using fourier techniques.
复制标题
使用傅立叶技术计算蛋白质对接的分子表面相关性。
DOI：
10.1142/s0219720007002916
复制
发表时间：
2007
影响因子：
1
通讯作者：
Sakk,Eric
中科院分区：
文献类型：
--
作者：
Sakk,Eric
The computation of surface correlations using a variety of molecular models has been applied to the unbound protein docking problem. Because of the computational complexity involved in examining all possible molecular orientations, the fast Fourier transform (FFT) (a fast numerical implementation of the discrete Fourier transform (DFT)) is generally applied to minimize the number of calculations. This approach is rooted in the convolution theorem which allows one to inverse transform the product of two DFTs in order to perform the correlation calculation. However, such a DFT calculation results in a cyclic or "circular" correlation which, in general, does not lead to the same result as the linear correlation desired for the docking problem. In this work, we provide computational bounds for constructing molecular models used in the molecular surface correlation problem. The derived bounds are then shown to be consistent with various intuitive guidelines previously reported in the protein docking literature. Finally, these bounds are applied to different molecular models in order to investigate their effect on the correlation calculation.
