Graphics Workstations and Networking Equipment for Structure Determination Using Parallel Computer

我们要求为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提供资金。该装置是利用并行计算机测定具有高度非晶体对称性的生物大分子组装体的晶体结构所必需的。这种计算密集的研究需要开发并行程序和问题求解环境，以促进对并行计算机的访问。到目前为止，我们的大部分工作都集中在原子分辨率下的病毒结构分析上。这项工作将扩大到研究各种生物结构，如蛋白质和蛋白质核酸复合体。到目前为止，我们的程序开发工作主要集中在电子密度平均和修正，以及傅立叶合成和分析。现在将通过并行化最初由普渡大学开发的程序来将注意力转移到数据处理上。人们希望这些程序，作为第一批结晶学并行程序开发，将被广泛采用。目前的界面将得到改进，以便于访问结构生物学程序套件，并扩大程序的任务范围。已经表明，并行计算使执行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经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和昆虫新村病毒。因此，有理由预计，这些发展将对执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，如果对结构有更好的了解，病毒的过程可能会停止。为了满足我们小组的计算需要，普渡大学于1994年5月购买了140个计算节点的Paragon系统，并为这项提议提供了200000美元的费用分摊。

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.