Nucleic acid modeling tool (NAMOT): an interactive graphic tool for modeling nucleic acid structures.

The helical nature of the molecule (almost all of the DNA and a significant portion of the RNA) makes the modeling of nucleic acids a unique task. Unlike other biopolymers (proteins, lipids, etc.), the integrity the structure of a nucleic acid molecule depends strongly on the maintenance of the base pairing within the molecule. Structural alterations (bending, stretching, compressing, etc.), in general, should not disturb the base pairings. A custom-made molecular modeling tool is developed taking into consideration this specific property of the molecule. Instead of Cartesian coordinates, the modeling is carried out on a set of reduced coordinates developed here in our laboratory. One of the advantages using this set of reduced coordinates is the readiness of maintaining the base pairings while altering the structure. A graphic routine is incorporated into the package to display the image of the molecule while the modeling work is being executed. The program is written in C using XView tool kit with Xlib routines to ensure portability to different workstations.