Graphics Workstations and Networking Equipment for Structure Determination Using Parallel Computer

我们要求为图形工作站和高速网络设备的资金将安装在普渡大学的生物科学和计算机科学部门。这些设备是必要的， 的 测定 的 晶体 结构 的 生物大分子组装与高水平的非晶体对称性使用并行计算机。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，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。这项工作将扩大到检查所有类型的生物结构，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，傅立叶合成和分析。现在将注意力集中到通过并行化最初在普渡大学开发的程序来进行数据处理。 希望这些方案，其中 的 第一个晶体学并行程序的发展，将成为广泛采用。目前的界面，允许方便地访问该套件的结构生物学程序是要改进和程序的任务范围，是要扩展。 已经表明，并行计算使得执行以前超出合理范围的任务成为可能。 因此，这些方案的可用性一直是 的 溶液 各种各样的困难 病毒 结构确定例如， 人柯萨奇病毒B3和昆虫野田村病毒。因此，可以合理地预期，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求，普渡大学于1994年5月购买了一个140个计算节点的Paragon系统，并为此提议提供了20万美元的费用分摊。

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.