POWRE: Protein Docking With Binding Free Energy Target Functions

这个项目的主要目标是开发算法和软件来模拟蛋白质分子与其所附着的分子（配体）的结合。鉴于受体和配体的三维结构，将开发快速可靠的计算方法来定位结合位点并预测复合物的几何形状。第一个具体目标将是适应现有的用于平移搜索的快速傅立叶变换算法，使用自由能目标来提高预测可靠性。第二个目标是开发旋转搜索的快速傅里叶变换方法。最后，这些方法将在蛋白质复合物数据库上进行测试和基准测试。根据结果，数据库连同算法将通过万维网提供。对于提交单体数据的研究人员，网络服务器将在波士顿大学计算科学中心的超级计算机上运行FFT对接算法的并行版本。

The broad goal of this project is to develop algorithms and software for modeling the binding of a protein molecule with the molecule to which it attaches (ligand). Given the 3-D structures of the receptor and the ligand, rapid and reliable computational methods to locate the binding sites and predict the geometry of the complex will be developed. The first specific goal will be to adapt existing Fast Fourier Transform algorithms developed for the translational searches to use free energy targets for improved predictive reliability. The second goal is to develop Fast Fourier Transform methods for rotational searches as well. Finally, the methods will be tested and benchmarked on a database of protein complexes. Based on the outcome, the database along with the algorithms will be will be made available via the World Wide Web. For researchers who submit monomeric data, the web server will run the parallel version of the FFT docking algorithms on the supercomputers in the Center for Computational Science at Boston University.