Massively parallel computation has continued to be a significant portion of the past years research effort. The 16,384 processor MP-2 utilization has increased to about 60%. This includes the continued exploration of algorithms that have been developed and adapted to the MasPar, including the genetic algorithm, a very fast version of the suboptimal dynamic programming algorithm for RNA structure prediction, a very fast and sensitive sequence comparison algorithm for determining sequence homologies in proteins and nucleic acids, a visual docker for docking drugs with a protein substrate and the development of a molecular dynamics program. In addition, work has continued on the heterogeneous RNA structure analysis system with further improvements in its graphical presentation capabilities, RNA database matching facilities, mutated structure generation and extensions to the MasPar interface. In addition, the port of the system to a Silicon graphics front end has been completed. The above system, in conjunction with gel shift experiments, RNase mapping studies and ultracentrifugation has been used to help determine the binding site of nucleocapsid protein NCp7 of HIV-1 and the RNA structural components that determine this site. This protein is important for encapsidation of the virus genome, RNA dimerization and primer tRNA annealing in vitro. Work has also progressed in using the genetic algorithm and the RNA workbench to study the structure of coxsackievirus and its relationship to cardiovirulence.
