This study addresses the problem of modelling loops in three-dimensional RNA structures using fragments taken from other RNA molecules. In the field of protein modelling, the value of using structural fragments taken from known molecules is well established. This relies on the fact that similar structural conformations have been observed in different proteins in different structural contexts. A similar comparative modelling approach could be useful for modelling homologous RNA structures. In this work, a fragmentbased approach to modelling RNA loops has been implemented and tested by
remodelling parts of a known tRNA molecule using loops taken from other known RNA structures. This approach has been used to suggest possible conformations for loops that are missing from the crystal structure of RNA component of Thermotoga maritima ribonuclease P. |