Graphics Workstations and Networking Equipment for Structure Determination Using Parallel Computer

我们请求资助在普渡大学生物科学系和计算机科学系安装图形工作站和高速网络设备。该设备是利用并行计算机测定具有高水平非晶体对称性的生物大分子组合的晶体结构所必需的。这种计算密集型的研究需要开发并行程序和解决问题的环境，以方便访问并行计算机。到目前为止，我们的大部分工作都集中在原子分辨率的病毒结构分析上。这项工作将扩展到检查各种生物结构，如蛋白质和蛋白质核酸复合物。到目前为止，我们的程序开发工作一直集中在电子密度平均和修改，以及傅里叶合成和分析。现在，我们将把注意力放在普渡大学最初开发的并行程序的数据处理上。希望这些程序作为第一批晶体学并行程序的发展，将被广泛采用。目前的界面，允许更容易地访问结构生物学程序套件，有待改进，程序的任务范围有待扩大。已经证明，并行计算使以前超出合理范围的任务成为可能。因此，这些程序的可用性已成为解决各种困难的病毒结构确定的重要组成部分，例如人类柯萨奇病毒B3和昆虫野田村病毒。因此，有理由预计，这些发展将对进行基本和必要生命过程的复杂生物分子的研究产生重大影响，并对病毒的研究产生重大影响，这些病毒的过程可能因对结构有了更好的了解而停止。为了响应我们小组的计算需求，普渡大学于1994年5月获得了140个计算节点的Paragon系统，并为该提案提供了20万美元的成本分摊。

We request funding for graphics workstations and high speed networking equipment to be installed in the Biological Sciences and Computer Sciences Departments at Purdue University. This equipment is necessary for the determination of crystal structures of biological macromolecular assemblies with a high level of non-crystallographic symmetry using the parallel computers. Such computationally intensive studies require the development of parallel programs and problem solving environments which facilitate access to parallel computers. Most of our work has focused so far on the analyses of virus structures at atomic resolution. This work will be expanded to examine all kinds of biological structures such as proteins and protein nucleic acid complexes. Until now, our program development efforts have been concentrated on electron density averaging and modification, and on Fourier syntheses and analyses. Attention will now be directed to data processing by parallelizing programs originally developed at Purdue University. It is hoped that these programs, among the first crystallographic parallel program developments, will become widely adopted. The current interface, permitting easy access to the suite of structural biology programs is to be improved and the range of tasks of the programs, is to be extended. It has already been shown that parallel computing has made it possible to perform tasks that were previously out of reasonable range. Thus the availability of these programs has been an essential component in the solution of a variety of difficult virus structure determinations e.g., the human Coxsakie virus B3 and the insect Nodamura viruses. It is therefore reasonable to anticipate that these developments will have a major impact in the study of complex biological molecules that perform basic and essential life processes, and on the study of viruses whose processes might be halted given a better knowledge of structure. In response to the computing needs of our group, Purdue University acquired a 140 compute node Paragon system in May 1994 and is providing $200,000 in cost sharing for this proposal.