PBM - A SOFTWARE PACKAGE TO CREATE, DISPLAY AND MANIPULATE INTERACTIVELY MODELS OF SMALL MOLECULES AND PROTEINS ON IBM-COMPATIBLE PCS

The PBM package was developed to create, display and conveniently mani pulate protein and small molecule structures on IBM-compatible microco mputers. It consists of four modules: CREATE, SPHERE, RIBBON and CONVE RT. CREATE includes commands to create or alter ('mutate') the primary and subsequently the tertiary structure of a given peptide or protein by defining phi and psi angles of residues at will, options to add, d elete or alter atoms in a structure, utilities to choose easily betwee n the most common rotamers of amino acid residue sidechains and option s to analyse in various ways a protein conformation. SPHERE provides f or an interactive manipulation of structures containing up to 2700 ato ms which can belong up to six different molecules. All manipulations c an be made with the use of an ordinary mouse, by choosing from a varie ty of pull-down menus. Three types of models can be implemented to dis play molecules on the computer screen or the plotter: skeletal, solid space-filling and wireframe space-filling models. RIBBON creates ribbo n models of proteins and allows for a limited variety of interactive m anipulations. CONVERT is a file converter, which is capable of convert ing files of atom coordinates of literally any format to Brookhaven Da ta Bank format files. The package produces very good results for prote in molecules of reasonable sizes, both in terms of graphics quality an d speed of operations, an an 80486 IBM PC-compatible machine equipped with a 1 MByte VGA display card and a colour VGA monitor, which is a r ecommended configuration.