MANIP: an interactive tool for modelling RNA

Abstract

Large RNA structures can be viewed as assemblies of smaller units or modules that are usually clearly identified (helices, hairpin loops, other recurrent motifs, etc.). We have developed a program, MANIP, which allows the rapid assembly of separate motifs (each with a specified sequence) into a complex three-dimensional architecture. The already determined modules are present in a database from which they can be extracted with the appropriate sequence. Their assembly is performed in real time on the computer screen with buttons and dials that command rotation and translation of any chosen fragment with respect to the chosen pivot, or that generate all possible variations of any torsion angle within a specified segment either in the 5' or in the 3' direction. The possible in-built manipulations follow the general stereochemical rules of RNA structure. MANIP automatically recognizes and displays the allowed and nonallowed hydrogen bonds between the residues. The program is interfaced with a rapid and automatic online refinement tool of partial or full assemblies, NUCLIN-NUCLSQ. The refinement protocol incorporates canonical as well as noncanonical base pairing constraints together with restraints imposed by covalent geometry, stereochemistry, and van der Waals contacts. The computer package runs on UNIX Silicon Graphics workstations and is written in C with OpenGL and X11/Motif libraries.