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It can be a tremendous advantage to have the X-ray crystal structure of a protein that is targeted for drug discovery. Due to recent advances in methods, software and hardware, crystallographic structure determination no longer requires a specialist in the method, but rather it has become a technique that can be readily applied to many research problems. The high-throughput approaches developed and used by structural genomics projects can be adapted and used to aid drug discovery efforts. It should be emphasized, however, that one cannot blindly accept the results of automated approaches and that it is essential to carefully validate the model, which is the interpretation of the observed electron density. It is important to be sure that it correctly describes the structure. The investigator that wishes to make use of the extensive database of protein structures in the Protein Data Bank (PDB) also needs to be know how to evaluate structural models, understand how they are related to the experimental data and be able to utilize computer graphics programs to look at the electron density distribution together with the model. [ABSTRACT FROM AUTHOR]

This chapter gives an overview over the current methods for automated modeling of RNA structures, with emphasis on template-based methods. The currently used approaches to RNA modeling are presented with a side view on the protein world, where many similar ideas have been used. Two main programs for automated template-based modeling are presented: ModeRNA assembling structures from fragments and MacroMoleculeBuilder performing a simulation to satisfy spatial restraints. Both approaches have in common that they require an alignment of the target sequence to a known RNA structure that is used as a modeling template. As a way to find promising template structures and to align the target and template sequences, we propose a pipeline combining the ParAlign and Infernal programs on RNA family data from Rfam. We also briefly summarize template-free methods for RNA 3D structure prediction. Typically, RNA structures generated by automated modeling methods require local or global optimization. Thus, we also discuss methods that can be used for local or global refinement of RNA structures. [ABSTRACT FROM AUTHOR]