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© Oxford University Press

DNA Modeller: an interactive program for modelling stacks of DNA base pairs on a microcomputer

Josef Jursa

Institute of Biophysics, Czech Academy of Sciences Královopolská 135, 61265 Brno, Czech Republic

DNA Modeller is a microcomputer program for interactively manipulating up to 20 bp in a DNA double helical arrangement. It calculates the van der Waals and electrostatic energies of base-base interactions using the AMBER potential, minimizes the energy with respect to the pair (buckle, propeller, opening, shear, stretch, stagger) and step (tilt, roll, twist, shift, slide, rise) parameters, calculates lengths of the canonical hydrogen bonds between the complementary bases, and calculates interatomic distances between the successive base pairs. Input/output files are simple lists of the step and pair parameters or lists of the atom specifications (N1, C2, etc.) and their Cartesian coordinates (compatible with the Desktop Molecular Modeller *.mol files). The program is supplied with a readbrk utility which transforms PDB/NDB to the*.mol format readable by DNA Modeller. The DNA crystal structures deposited in the PDB or NDB databases can thus be analyzed, and their bases visualized and interactively manipulated. In addition, DNA Modeller can calculate the base pair and step geometrical parameters and interaction energies. A plotter utility creates wire mono or stereo pictures of the bases. This program is designed for IBM-compatible computers working under DOS or can run as a DOS application under MS Windows 3.x or Merge (SCO Unix DOS emulator).

Received on July 27, 1993; accepted on October 12, 1993

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