NUCPLOT - A PROGRAM TO GENERATE SCHEMATIC DIAGRAMS OF PROTEIN-NUCLEICACID INTERACTIONS

Proteins that bind to DNA are found in all areas of genetic activity w ithin the cell, To help understand how these proteins perform their va rious functions, it is useful to analyse which residues are involved i n binding to the DNA and how they interact with the bases and sugar-ph osphate backbone of nucleic acids, Here we describe a program called N UCPLOT which can automatically identify these interactions from the 3D atomic coordinates of the complex from a PDB file and generate a plot that shows all the interactions in a schematic manner. The program pr oduces a PostScript output file representing hydrogen, van der Waals a nd covalent bonds between the protein and the DNA, The resulting diagr am is both clear and simple and allows immediate identification of imp ortant interactions within the structure, It also facilitates comparis on of binding found in different structures, NUCPLOT is a completely a utomatic program, which can be used for any protein-DNA complex and wi ll also work for certain protein-RNA structures.