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© Oxford University Press

PBM: a software package to create, display and manipulate interactively models of small molecules and proteins on IBM-compatible PCs

A. Perrakis 1, C. Constantinides 2, A. Athanasiades 3 and S.J. Hamodrakas 4

Department of Biochemistry, Cell and Molecular Biology and Genetics, University of Athens Panepistimopolis, Athens 15701, Greece

4To whom reprint requests should be sent

The PBM package was developed to create, display and conveniently manipulate protein and small molecule structures on IBM-compatible microcomputers. It consists of four modules: CREATE, SPHERE, RIBBON and CONVERT. CREATE includes commands to create or alter (‘mutate’) the primary and subsequently the tertiary structure of a given peptide or protein by defining {varphi} and {psi} angles of residues at will, options to add, delete or alter atoms in a structure, utilities to choose easily between the most common rotamers of amino acid residue sidechains and options to analyse in various ways a protein conformation. SPHERE provides for an interactive manipulation of structures containing up to 2700 atoms which can belong up to six different molecules. All manipulations can be made with the use of an ordinary mouse, by choosing from a variety of pull-down menus. Three types of models can be implemented to display molecules on the computer screen or the plotter: skeletal, solid space-filling and wireframe space-filling models. RIBBON creates ribbon models of proteins and allows for a limited variety of interactive manipulations. CONVERT is a file converter, which is capable of converting files of atom coordinates of literally any format to Brookhaven Data Bank format files. The package produces very good results for protein molecules of reasonable sizes, both in terms of graphics quality and speed of operations, on an 80486 IBM PC-compatible machine equipped with a 1 MByte VGA display card and a colour VGA manitor, which is a recommended configuration.

Received on June 21, 1994; revised on November 11, 1994; accepted on November 11, 1994

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