Macromolecular marionettes

Computer graphics can provide useful tools for molecular biology because pictorial displays are the most efficient way for computers to communicate the details of a complex molecular structure to human beings. The development of suitable hardware has led to the establishment of a number of computer graphics installations devoted to the investigation of molecular structure. We describe here the Evans and Sutherland LDS-1 PDP-10 system of the Princeton University Computer Graphics Laboratory, and the program systems that we have developed for applications to the study of protein and nucleic acid structure and interaction. The hardware can generate displays of complicated three-dimensional line drawings. It allows interactive analysis and modification of a display by a human observer, as well as computational analysis of structural data by a powerful general-purpose digital computer, the PDP-10. We have developed programs for the study and analysis of proteins and nucleic acids of known structure, and for construction and experimentation with models of general polypeptides and polynucleotides. These model-building programs permit the generation of displays of polypeptides and polynucleotides of arbitrary sequence and conformation. It is possible to adjust all conformational angles interactively, or with the assistance of supportive software that can carry out a variety of structural manipulations, such as the folding of a selected region into a helical conformation. Although the purely computational problems encountered in this work are relatively straight-forward-a tribute to the power of the equipment-subtle problems arise in defining the role of a human being as a partner in the execution of an interactive program. Our attempts to achieve the most effective combination of human and computers depend on the recognition of the strengths and limitations of each, and of the efficiencies of the channels of communication between them.