Abstract:
:Proteins that bind to DNA are found in all areas of genetic activity within the cell. To help understand how these proteins perform their various functions, it is useful to analyse which residues are involved in binding to the DNA and how they interact with the bases and sugar-phosphate backbone of nucleic acids. Here we describe a program called NUCPLOT 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 produces a PostScript output file representing hydrogen, van der Waals and covalent bonds between the protein and the DNA. The resulting diagram is both clear and simple and allows immediate identification of important interactions within the structure. It also facilitates comparison of binding found in different structures. NUCPLOT is a completely automatic program, which can be used for any protein-DNA complex and will also work for certain protein-RNA structures.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Luscombe NM,Laskowski RA,Thornton JMdoi
10.1093/nar/25.24.4940subject
Has Abstractpub_date
1997-12-15 00:00:00pages
4940-5issue
24eissn
0305-1048issn
1362-4962pii
gka795journal_volume
25pub_type
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