N U C P L O T manual

1. Introduction

NUCPLOT is a program that automatically generates schematic 2D representations of protein-nucleic acid interactions. The input is a standard PDB file and the output is a colour or black-and-white PostScript file which gives a simple, at-a-glance representation of the hydrogen bonds and hydrophobic contacts between proteins and nucleic acids.

By default, NUCPLOT expects the hydrogen bonds and non-bonded contacts to be calculated by the HBPLUS program (McDonald & Thornton, 1994) and can read files output by that program. It is possible to use data computed by other means provided they are supplied in the format described in Appendix B.

HBPLUS was primarily designed for calculating interactions within large molecules found in the PDB. This means that it is unable to recognize the majority of small ligands and as a result may miss certain hydrogen bonds between the protein, nucleic acid and ligand. This would result in plots lacking the required small molecule-nucleic acid interactions.

HBPLUS does allow the user to define ligands in a separate input file as described in the HBPLUS Operating Manual. The file describes the nature of hydrogen bonds each atom in the ligand is able to make and therefore allows HBPLUS to correctly calculate the interactions to it.

A program called HBADD is supplied which aims to reduce the work involved in creating this input file for HBPLUS. The program looks for any HETATM records in a given PDB file and searches for its' structure in the Het Group Dictionary. The input file is then created. The Het Group Dictionary is available directly from the wwPDB at:

The script file provided in the package automatically runs HBADD, HBPLUS and NUCPLOT. We recommend the use of this script for producing your plots.

N U C P L O T manual