Aims

• To introduce bioinformatics challenges in analysing and predicting the three-dimensional structures of RNA molecules.
• To mention some past Masters projects in the area of structural bioinformatics, and some topics for future projects.

Objectives

After this lecture you will:

• be aware of computational approaches to modelling the three-dimensional structures of RNA molecules.

Supplementary Material

Some approaches to building three-dimensional RNA structures are described in:

Major F. "Building three-dimensional ribonucleic acid structures", Computing in Science and Engineering, 2003; 5(5):44-53 (IEEE Xplore)

In recent years there have been several papers describing RNA structure analysts, including studies of base pair geometries:

Leontis NB, Westhof E. "Geometric nomenclature and classification of RNA base pairs", RNA. 2001 Apr; 7(4):499-512 (PubMed)

and backbone conformation:

Murray LJ, Arendall WB 3rd, Richardson DC, Richardson JS. "RNA backbone is rotameric", Proc Natl Acad Sci U S A. 2003 Nov 25; 100(24):13904-13909 (PubMed)

Past Masters projects in the area of structural bioinformatics include:

• ^* "STACK: a toolkit for analysing beta-helix proteins", Salvatore Cappadona and Lars Diestelhorst
• ^* "Structural Identification of Immunoglobulin Variable Domains", Huihua Li
• "Graphical representation of MHC molecules", Mats Krantz
• ^* "Prediction of Oligosaccharide 3D Structure using Genetic Algorithm Search Methods", Abraham Nahmany and Francesco Strino
• "ALIGNER: A Toolkit for Protein Structure Comparison", Mats Eriksson
• "Extensions to RasMol to Support Analysis of Protein Waters", Jonas Malmsten
• ^* "Structure and sequence studies of fucose binding sites", Mun Gwan Hong

^* These are available in the archive of Masters theses.

I am interested in supervising student projects in the areas of Bioinformatics and Databases (local access only).